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Semantic Web Applications and Tools for Life Sciences Hackathon

A two day event hacking content, systems and services for the Life Sciences

University of London Union, Malet Street, Bloomsbury, London, WC1E 7HY.

Tuesday 6th December and Wednesday 7th December, 2011.

This FREE hackathon has been co-organized by DevCSI (JISC Funded), SWAT4LS and Open Knowledge Foundation  bringing together delegates from the SWAT4LS workshop and tutorials (taking place on the 8-9 December 2011) and researchers, developers and anyone else interested in the Life Sciences to work together in teams or individually to use and enhance exisiting Open Science semantic web applications and tools and possibly develop new ones. The event will be suitable for:
  • Researchers in the Life Sciences
  • Software developers in the Life Sciences
  • Software developers / researchers developing Semantic Web Applications / Tools / Mashups / Visualisations from the Life Sciences and other domains
  • Anyone interested in developing and using Open Science tools particularly in the Life Sciences
  • Those offering support for using data sets, APIs and tools to be used for the delegates
We hope that delegates and even those not able to make the event will be able to discuss and propose ideas, suggest tools, share datasets, invite collaborations BEFORE the event using the OKFN Open Science Mailing List and OKFN wiki (see below).

The event will start at 6pm on Tuesday 7th December, where we will encourage participants to present lightning talks, network, share ideas, form teams, and think about what they will be working on for the next day. Ideally it would be great if you could start to think of some areas of interest before the event. The next day will start at 9am with teams and individuals outlining their ideas and then they will be given approxiamtely 6-7 hours to work on them. All teams and individuals will be invited to present what they have been working on and the best three ideas/prototypes will be awarded special prizes.

We are working closely with the organisers of  SWAT4LS, OKF to ensure that the hackathon can be the best it can be and we have already started thinking of some ideas which you are welcome to start on:

Malaria Research

OKF are suggesting that an area of interest could be the integration and elaboration of disease specific information, specifically malaria research, with outputs being scaleable to other diseases.

The aim is for individuals / teams to develop a corpus of accessible, semantically linked and enriched information on the current body of research into this major disease which will be of benefit to both scientists and citizens. Tasks will include gathering information from several web sources, including open bibliographic data and open access scientific literature, annotation of the collected data and the generation of interfaces, mashups and visualizations to increase functionality and demonstrate use cases. For example, allowing community annotation of research publications. OKF suggest that you will gain experience working with linked open data using common vocabulary and a wide range of standard and semantic web tools.

- To generate a high quality set of reports on disease research, available openly to anybody.
- To build upon that base by annotations and mash ups of the underlying information.

- Gather information on the current open body of malaria research
- Generate open research reports on a subset of papers using the Minimal Information reporting standard for an Infectious Disease Investigation (MIIDI) and input schema at the University of Oxford

UK PubMedCentral Bibliographic Data
Open Bibliography/Open Citation Data

Open Research Reports XML schema and input form

Other diseases of particular interest are Cancer and Creutzfeldt–Jakob disease (CJD). Please let us know if you are interested in working on these two diseases or other ones by emailing the organisers.

Mailing list to discuss ideas before, during and after the event

We strongly encourage you to discuss what tools and data sets to be used etc well before the event, by subscribing to the mailing list by visiting


OKF have now created a wiki to start putting ideas together for the event:, this will be used before, during and after the event.


Collaborative online note 'Pads' will be available on the day for real time collaboration, the notes of which will be migrated on to the wiki after the event, see:

Tag for event



You will be able to follow announcements about the event via twitter (as well as feeds from blogs and websites etc) by searching for the above tag. If you are new to twitter, please visit, and create an account for yourself. We will be using technologies like this frequently, before, during and after the event.

If you require a twitter client (software to keep up to date with the latest twitters), several can be found at