1. SWAT4LS 2009, Semantic Web Applications and Tools for Life Science workshop in Amsterdam, 2009 2. Concept Web Alliance

1. SWAT4LS 2009Semantic Web Applications and Tools for Life Sciences http://www.swat4ls.org/ Amsterdam, Science Park, Friday, 20th of November 2009

2. Topics of interest Standards, Technologies, Tools for the Semantic Web Systems for a Semantic Web for Bioinformatics Existing and prospective applications of the Semantic Web for Bioinformatics 2

3. Deadlines Tue 1st September: Submission opens Mon 28th September: Paper submission Fri 23rd October: Communication of acceptance Fri 6th November: Revised paper Fri 20th November: SWAT4LS Workshop 3

4. Concept Web Alliancehttp://www.conceptweballiance.org/ Towards the Concept Web The dynamic, interactive fabric of concepts in science, and their relations … for and by scientists Critical slides by Carole Goble

5. Concepts 5

6. Triples = ‘factoids’ 6 Inhibits

7. Factoids as mini-publications 7 Stated by

8. What is CWA? A Forum: to unite stakeholders to share complex Life Science data in a new way, through triples. A Facilitator: to promote the development of triple content services and promote the development of triple professional services. A Facility: A “warehouse”, distributor and agent for triples on behalf of contributors and users. Develop our own services.

9. http://blog.larkc.eu/?tag=linked-data-cloud + + + Linked Open Data

10. Start Small. Incremental Value. One thing well.Triples. Triples. Triples. Jam today. More Jam Tomorrow.

11. Some initial ideas Focus on what we talk about Focus on factoids Machine readable for use in our applications Bottom-up standardization / certification 11

12. Where significant value is added…suggestions …triples represent an economic value and can be charged for Curated triples: charges at the discretion of the curator Inferred triples: charges at the discretion of the inferrer Disambiguated triples: charges at the discretion of disambiguator Redundancy-removed triples: charges at the discretion of the redundancy remover Observed triples can be charged for if they are taken from proprietary sources – by or on behalf of the proprietors peer-reviewed literature: charges at the discretion of the rights-holder

14. Protein databases (UniProt, IntAct, PDB, HPRD – 75,000 human curated PPIs) (from public data)

15. Gene (co-expression databases (GEO, Express… – 25 square genes) (from public data)

16. STRING edges (200,000 gene-gene edges) (from semi public data)

17. InWeb edges (240,000 unique edges from 17 species) (from proprietary data)

18. Reactome edges (240,000 unique edges from 17 species) (from proprietary data)

19. Chemspider edges (25,000,000 chemicals) (from semi public data)

20. Wiki edges (WikEdge = WikiPathways, WikiProfessionals, Omegawiki, Wikigene)

21. Plectix edges (5,000 extra edges (PPI modeling) (from proprietary data)

22. Private expression data (3000 extra edges, by Merck) (from proprietary data)

24. Participation on the journey… Organisation governs community driven creation of concept web Think about: Is the CWA useful to you / your organisation? Would you subscribe? Why? / Why not? How would you like to participate? Would you help us develop the Alliance? You rule!

25. http://www.conceptweballiance.org/ 16 Barend Mons Marco Roos Carole Goble Katy Wolstencroft http://www.conceptweballiance.org/