= UseCases =

== Participants ==
(Please add your name!)

  * Kazuharu Arakawa
  * Mark Wilkinson
  * Francois Belleau
  * Arek Kasprzyk
  * Paul Gordon
  * Yasunori Yamamoto
  * Akira R. KINJO
  * Gos Micklem
  * Shuichi Kawashima
  * Erick Antezana (dropping by ...)

== Summary ==

Lots of use cases in data and service integrations are available in websites such as [http://www.myexperiment.org/ myExperiment] and [http://www.flymine.org/ FlyMine]. Using semantic web, any of the existing questions and use cases can be more efficient.

So one use case/demonstration would be to compare how data can be published with existing & SW technology.

= Cases where semantic web is more fruitful =

  * questions that queries over separated DBs
    * using in-house data -> NGS
    * can be in different sources - less cost of integration
    * small DBs (as opposed to NCBI, EBI, and KEGG)
  * querying the predicates
    * discovery of DBs
    * hypothesis generation
  * interpreted knowledge
    * not numerical?
    * not too raw?
    * linked by predicates (even if numerical)
  * data are linked
  * users do not have to know the entire schema

= possible use cases? =

  * migrate SQL to simple SPARQL endpoints
    * easy to convert 20 lines?
    * convert PDB relational to Sparql (kinjo-san, Francois)
    * miRbase (raoul)
  * Paul (biological hypothesis formulation)
    * predict PPI using homologs (PPI in yeast -> homolog in human) see [http://www.biomedcentral.com/1471-2164/9/426]
    * workflow overview: could use homolog, protein domain and protein-protein interaction resources (not all currently in one data warehouse so Sem Web could help)
[[Image(http://www.biomedcentral.com/content/figures/1471-2164-9-426-1.jpg)]]

  * formulation of SPARQL queries -> RDFscape
    * can be GUI.