HCLS/SWAT4LS2012/Hackathon

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The SWAT4LS Hackathon is an informal event associated with the SWAT4LS Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions. The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (map).

street: 151 rue Montmartre, Passage des Panoramas
room: 12 Galerie Montmartre
75002 Paris

(For more information, please refer to the workshop website). The hackathon is open to workshop participants. Registration is required and space is limited!.

Logistics

Projects and institutes attending include:

While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

Information and registrations

For information, info _at_ swat4ls.org

Registrations are handled via Eventbrite

Hashtag

#swat4lshack

Co-Organizers

  • Andrea Splendiani
  • Andra Waagmeester
  • Eric Prud'hommeaux
  • Toshiaki Katayama
  • Ismael Navas delgado

Open PHACTS community

Contact Point

  • Andra Waagmeester
  • Egon Willighagen

Proposed action points

  1. Consume Open PHACTS content in Pathway tools
  2. Using http://identifiers.org
  3. Create an example set of valuable queries
  4. Visualizing output
  5. work on further linked data integration, with possible:
    1. DrugMatrix
    2. TG-GATEs
    3. CTD (already available as RDF, by Bio2RDF)
  6. shared Java client code
    1. for R, Bioclipse, KNIME

Confirmed Participants

  • Kees Burger
  • Maria Carmen Carra
  • Ian Dunlop
  • Chris Evelo
  • Paul Groth
  • Tim Harder
  • Carina Haupt
  • Nick Juty
  • Camille Laibe
  • Antonis Loizou
  • Oriol Lopez
  • Guillermo C. Martínez
  • Nuria Queralt
  • Rishi Ramgolam
  • Mark Thompson
  • Egon Willighagen
  • Pekka Kohonen

WikiPathways community

Contact Point

Andra Waagmeester

Introduction

WikiPathways is a online resource for pathways. Content is provided by the audience at large. I currently contains more then 2200 pathways from 21 species source. Pathways are captured in a XML-based format GPML. Recently WikiPathways was exposed as linked open data where GPML content was exported as RDF. This data is available through a SPARQL endpoint http://sparql.wikipathways.org.

Proposed action points

  1. Exploring WikiPathways RDF content, making example queries
  2. Writing federated queries to integrate pathway content with other biological data.
  3. Using Pathvisio RPC.

Confirmed Participants

  • Chris Evelo
  • Martina Kutmon
  • Alex Pico

Database Center for Life Sciences Community / BioHackathon

Contact Point

Toshiaki Katayama

Proposed action points

W3C HCLS Community

Contact Point

Eric Prud'hommeaux

Proposed action points

BioPAX Community

Contact Point

Ismael Navas Delgado

Proposed action points

Confirmed Participants

  • Ismael Navas Delgado
  • Andrea Splendiani

Resources

  • PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
  • Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
  • BioQueries: social site to build SPARQL queries
  • Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/