Difference between revisions of "HCLS/SWAT4LS2012/Hackathon"

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(Data Map)
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* Egon Willighagen
* Egon Willighagen
* Pekka Kohonen
* Pekka Kohonen
* Ola Spjuth
== WikiPathways community ==
== WikiPathways community ==

Revision as of 10:21, 26 October 2012

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!.


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




  • 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
  • Ola Spjuth

WikiPathways community

Contact Point

Andra Waagmeester


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

Exploring WikiPathways RDF content, making example queries

Writing federated queries to integrate pathway content with other biological data.

Using Pathvisio RPC to consume and visualize linked pathway data

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

Making an online inventory of available resources (wiki) to document underlying schemas of available datasources.

There are nice lists of active SPARQL endpoints (example 1) and (example 2). Finding where the data actually links can still be challenging.

It would be really beneficial to create an overview with descriptions of different linked data sets describing the underlying structure. The first step would be to define a format where data providers describe their data in a predefined (wiki) format. This format could be based on VoID. These description coulds then be used to create so called data landscapes in tools such as Semscape.

Creating a review of sparql endpoints and their support for remote federated queries.

Within a federated query you can query different flavours of sparql endpoints. SInce different endpoints have their own implementations and support for different SPARQL versions, it is essential to understand the different issues each type of endpoint might have. The community would benefit from a list mentioning each available SPARQL endpoint system (e.g. 4store, virtuoso, etc) and their support for different SPARQL versions. Also this list could mention specific features (e.g. soft limit in 4store) influencing the recall in federated queries.

BioPAX Community

Contact Point

Ismael Navas Delgado

Proposed action points

Confirmed Participants

  • Ismael Navas Delgado
  • Andrea Splendiani


  • 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/

Data Map

 @prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix skos:    <http://www.w3.org/2004/02/skos/core#> .
 @prefix dcterms: <http://purl.org/dc/terms/> .
 @prefix wprdf:   <http://rdf.wikipathways.org/> .
 @prefix foaf:    <http://xmlns.com/foaf/0.1/> .
 @prefix wp:      <http://vocabularies.wikipathways.org/wp#> .
 @prefix biopax:  <http://www.biopax.org/release/biopax-level3.owl#> . 
 @prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .    
 @prefix gpml:    <http://vocabularies.wikipathways.org/gpml#> .
 @prefix chembl:  <http://rdf.farmbio.uu.se/chembl/onto/#> .
 @prefix up:      <http://purl.uniprot.org/core/> .
 <http://sparql.wikipathways.org> {
    # Sparql endpoint: http://sparql.wikipathways.org
    # Data: http://rdf.wikipathways.org
   <http://identifiers.org/ncbigene/1051> rdf:type wp:GeneProduct .
   <http://identifiers.org/ncbigene/1051> dcterms:isPartOf wprdf:WP3 .
   <http://identifiers.org/ncbigene/1051> rdfs:label "C/EBP-beta" .
   wprdf:WP3 rdf:type wp:Pathway .
   wp:Pathway skos:relatedMatch biopax:Pathway .
   wprdf:WP3 rdfs:label "Keap1-Nrf2 Pathway" .
   wprdf:WP3 dcterms:description """Based on Surh, 2003, figure 4 Nrf2 induces the expression of many
     antioxidant enzymes. It is therefore thought to be involved in oxidative stress response."""^^xsd:string. 
   wprdf:WP3 <http://purl.org/pav/version> "48217"^^xsd:string .
   wprdf:WP3 gpml:biopaxref "dba" .
   wprdf:WP3 gpml:height "731.0"^^xsd:float .
   wprdf:WP3 gpml:width "914.0"^^xsd:float .
   wprdf:WP3 wp:category wp:CellularProcess .
   wprdf:WP3 wp:organism <http://identifiers.org/taxonomy/9606> .
   wprdf:WP3 wp:pathwayOntology <http://purl.obolibrary.org/obo/PW:0000378> .
   wprdf:WP3 foaf:page "http://www.wikipathways.org/index.php/Pathway:WP3" .
 <http://rdf.farmbio.uu.se/chembl/sparql> {
   chembl:something chembl:foo "bar"
 <http://beta.sparql.uniprot.org/> {
   up:something up:foo "bar"
 # parses up to here.
 :Textmining {
   :hit ao:fdgr "blabla"
 :Linksets {
   up:Q12345 skos:broadMatch end:000xxxxx .


Andra, you can even add tables of VoID stuff if that helps:

pav:createdOn "2012-10-25"^^xsd:date ;
void:foo void:bar .
pav:createdOn "2012-10-25"^^xsd:date ;
void:foo void:bar .