Working Groups/Science/swat4ls hackathon

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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.

Overview

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.

Target Audience

The event will be suitable for:

Programme

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 6th 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.

Full version of programme can be found here


Lightning Talks

See notes from all talks here http://wiki.okfn.org/Working_Groups/Science/swat4ls_hackathon/lightning

Participants

Once registered, please add your name expertise and what tools or resources you have that may be useful to other hackathon participants to the participant page [[2]]

Theme Ideas

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.

Please add your own ideas to the wiki below and feel free to create a separate page if you wish.

Open Disease Research Reports

Aims:

Objectives:


See the project page: http://wiki.okfn.org/Working_Groups/Science/swat4ls_hackathon/ORR

Gene-Drug Visualisation

Aims:


Objectives:


Results

Interactions.PNG Fig 1. Frequency of drug-target mode of actions

Drug2genes.png Fig 2. Drug-protein interaction network from drugbank. Blue are proteins; red are drugs

Disease Localiser

http://wiki.okfn.org/Working_Groups/Science/Disease_Localiser

Semantic Web Tools/Resources/Discussions

Other Ideas from Post it Notes

Responses… SPARQL end points, web interfaces and visualisation tools

To be useful for users (Biologists - clinicians)

Patients would access papers related to the searched disease and its synonyms.


Therefore it would would be useful to identify the sets of parameters and the level of values which in turn will allow to choose areas which will need a first action to be taken. The data should produce (on the global i.e. national or regional level) a set of indicators whether or not the particular case should be evaluated deeper (perhaps with the extended set of parameter). The starting point could be at the level of single patients case or based on the annual reports for whole countries. The answer given by the model could help to narrow the area where for some reason the problem is more likely going to encalate?

Teams and Tasks

Results

Round ups / Feedback talks

Express Open Citation via SADI - Mark Wilkinson et al

This group looked into putting a SADI wrap around citations to make them more searchable and finding a service that uses URI such as PubMed to return the metadata to create PubMed IDs automatically.

Visualising drug-to-protein interaction - Helena Deus et al, AKA 'The Dodgy Plotters'

These people created an RDP out of proteins. The first visualisation of this displays too much data at once but overall shows that drugs have many genes. The plan now is to make drugs proportionally bigger according to cost and show other types of drugs. The output diagram show labels when clicked.

Working Group around disease localiser - Tomasz Kluza et al

This group created a service to help with localisations and diseases. It was intended to concentrate on malaria but a service for this was found to be already available, which was based on data via news feeds, so attention was turned to cancer. A contact with the project was e-mailed, who makes information re diseases available on the web, and the team volunteered to assist in extend their services when it transpired this service is due to be stopped soon. A sample database of one type of cancer was established thanks to interaction and discussions with other members of the Hackathon. In relation to cancer, the group looked at the geographic spread of cancer in smokers and referred to healthmap.org.

Text Mining and the Large Knowledge Collider - Reinout van Schouwen

Reinault investigated using Peregrine, a text mining technology, and integrating this into TodoBox, the mining client. He looked at natural language within cancer research and how best to use this to compile data.

MIIDI, Cancer Investigations, BibSoup - Jenny Molloy et al

The group asserted that open research reports are a necessity for functionality in research as is access to bibliographic data. Their development was to create these connections. They took output in MIIDI form and put into BibSoup. They also took a list of document titles from cancer forums and put into PubMed and the metadata into BibSoup. They then examined the interface to show all the metadata, displays, time-line, map display etc. They looked at filtering data for patients - listing by side-effects, outcome, availability of the drugs etc - as well as adding a mechanism to upload lay summaries which would be sent by e-mail to the author for approval.

BioSPRKL Tools and Resources for RDF Search - David Gifford et al

This group developed a BioSPRKL system to query web modules. This analyses datasets and links, and automatically generates a user; another part of this resource works locally on the PC with datasets. Suggestions for improving the resulting user experience have been taken on board.

Literature Recommendations - Yasunori Yamamoto

Yasunori worked on TogoDoc, looking at the literature already available. SPRKL queries can pick up differences within literature and he examined integrating TogoDoc with Peregrine. When searching for papers and adding narrative to database link, data mining is very important and this research was to improve this system.

Suggestions for future events

Hold over 2 full days and include accommodation so time constraints are lessened;

Create a forum for lessons learnt;

Follow up on ideas that come to fruition, revisit in 6 months;

Every few hours, arrange a short break to feedback to the lead or note-taker for each Working Group who can keep notes on progress and bounce ideas around;

There is value in getting together without preamble, but ideal is combination of spontaneity and forethought;

As done by Peter Murray-Rust, stick a label on t-shirt stating area of interest, to encourage interaction around topics;

Find a good way to interrupt people mid-creative process, to find out what they're doing when they look busy - Etherpads should be mandatory for this purpose;

Rolling video-streams of Twitter, work ongoing etc, in background;

Have 'floating' people to put notes on WIKI when other people are busy perhaps using a flag system.


There will be feedback forms, please complete, and if you have ideas for sponsors or other events please get in touch with the organising group.

Communication

Mailing Lists

We strongly encourage you to discuss what tools and data sets to be used etc well before the event, by subscribing to the open-science@lists.okfn.org mailing list by visiting http://lists.okfn.org/mailman/listinfo

Wiki

You will all be provided with a login to this wiki, feel free to edit!

Pads

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: http://okfnpad.org/swat4ls-hackathon

Hashtag

Tag for event = #devcsi

Twitter

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, http://www.twitter.com 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 http://www.twitstat.com/twitterclientusers.html

Retrieved from "http://wiki.okfn.org/Working_Groups/Science/swat4ls_hackathon"
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