CWA & SWAT4LS Pitch at DILS2009

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

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
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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
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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

Concepts
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Triples = ‘factoids’
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Inhibits

Factoids as mini-publications
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Stated by

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.

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

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

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

Revenue generating
Download Concept Web triples
Includes edges from:

Pubmed (400,000,000 sentences, 5,000,000,000 concept co-occurrences) (from public data)
Protein databases (UniProt, IntAct, PDB, HPRD – 75,000 human curated PPIs) (from public data)
Gene (co-expression databases (GEO, Express… – 25 square genes) (from public data)
STRING edges (200,000 gene-gene edges) (from semi public data)
InWeb edges (240,000 unique edges from 17 species) (from proprietary data)
Reactome edges (240,000 unique edges from 17 species) (from proprietary data)
Chemspider edges (25,000,000 chemicals) (from semi public data)
Wiki edges (WikEdge = WikiPathways, WikiProfessionals, Omegawiki, Wikigene)
Plectix edges (5,000 extra edges (PPI modeling) (from proprietary data)
Private expression data (3000 extra edges, by Merck) (from proprietary data)
Et Cetera

Triple sales and Open Data/Open Access
Single triples:
free and open, via web search interface
revenue from advertising?
Collections:
at the discretion of owners
e.g. free if used publicly on web, with possibility of advertising revenue
paid-for if used behind firewall

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!

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