Beyond Open Access
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Transcript of Beyond Open Access
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KNEWCO
Please observe. In the space of one hundred and seventy-six years the Please observe. In the space of one hundred and seventy-six years the Lower Mississippi has shortened itself two hundred and forty-two miles. Lower Mississippi has shortened itself two hundred and forty-two miles. This is an average of a trifle over one mile and a third per year. This is an average of a trifle over one mile and a third per year. Therefore, any calm person, who is not blind or idiotic, can see that in Therefore, any calm person, who is not blind or idiotic, can see that in the Old Oolitic Silurian Period, just a million years ago next November, the Old Oolitic Silurian Period, just a million years ago next November, the Lower Mississippi River was upward of one million three hundred the Lower Mississippi River was upward of one million three hundred thousand miles long, and stuck out over the Gulf of Mexico like a thousand miles long, and stuck out over the Gulf of Mexico like a fishing-rod. And by the same token any person can see that seven fishing-rod. And by the same token any person can see that seven hundred and forty-two years from now the Lower Mississippi will be hundred and forty-two years from now the Lower Mississippi will be only a mile and three-quarters long, and Cairo and New Orleans will only a mile and three-quarters long, and Cairo and New Orleans will have joined their streets together, and be plodding comfortably along have joined their streets together, and be plodding comfortably along under a single mayor and a mutual board of aldermen. There is under a single mayor and a mutual board of aldermen. There is something fascinating about science. One gets such wholesale returns of something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact.conjecture out of such a trifling investment of fact.
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KNEWCO
Beyond Open AccessBeyond Open Access
Jan VelteropJan VelteropUKSG, Torquay, March 30, 2009
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KNEWCO
There is something fascinating about science.There is something fascinating about science.One gets such wholesale returns of conjecture out of One gets such wholesale returns of conjecture out of such a trifling investment of fact.such a trifling investment of fact.
Mark Twain, Mark Twain, Life on the MississippiLife on the Mississippi
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KNEWCO
What’s wrong?What’s wrong?
We have far too We have far too fewfew returns in terms of actionable returns in terms of actionable knowledge out of such overwhelming investment of knowledge out of such overwhelming investment of fact!fact!
The reason is that a lot of fact is deeply hidden!The reason is that a lot of fact is deeply hidden!
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KNEWCO
Current Knowledge Transfer Current Knowledge Transfer
Needle transportNeedle transport
An analogyAn analogy
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KNEWCO
Information overload?Information overload?
Too much knowledge?Too much knowledge?
Stop acquiring it?Stop acquiring it?
Or organisation underload?Or organisation underload?
Unprecedented opportunity?Unprecedented opportunity?
Just filtering it?Just filtering it?
Lack of conceptual structure?Lack of conceptual structure?
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KNEWCO
Information ‘overload’ will increaseInformation ‘overload’ will increase
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KNEWCO
Analogy:
What is the use of water?
Analogy:
What is the use of water?
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KNEWCO
H2OH2O
Drink(take in)
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KNEWCO
What is the use of information?What is the use of information?
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KNEWCO
Read(take in)
Age to KnowAge to Know
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KNEWCO
Publish articles
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KNEWCO
Publish articles
body composition
obesity
diabetes
QuickTime™ and a decompressor
are needed to see this picture.
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KNEWCO
Experienced in publishing articles
e.g. providing author proofs e.g. providing author proofs with proposed triples and with proposed triples and asking them to verify thoseasking them to verify those
e.g. providing author proofs e.g. providing author proofs with proposed triples and with proposed triples and asking them to verify thoseasking them to verify those
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KNEWCO
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KNEWCO
Living not on detail aloneLiving not on detail alone
Getting the big picture – too Getting the big picture – too
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KNEWCOInformation silos
MRSIndex, virtual concepts
Daily feed
UniprotPubMed
NextprotCALIPHO InWeb WikiPro SERMO
BioBankse.g. LOVD GEO GWA
CommunityAnnotation(a posteriori)
CommunityAnnotation(a posteriori)
<ID1><edge><ID2>
Triplet construction(unsupervised)
Direct feedBlogs, etc.
CommunityAnnotation(a priori)
Peregrine
Concept Mapping
Harmonized data
Biocommontology
Tools, RDF, OWL, OBO, Protégé
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KNEWCO
<Type F1> Database facts (multiple attributes) <Type F2> Community Annotations
<Type C1> Co-occurrence sentence (abstracts e.g. PubMed) <Type C2> Co-occurrence Full Text (publisher e.g. Springer)
<Type A1> Concept Profile Match <Type A3> Co-expression (gene expression Databases) <Type A4> Modelling hypothesis (e.g. Plectix, InWeb)
Graph Building (e.g. WikiPathways)
Multiple Triples
F+ C+ A+F+ C+ A+
C+ A+C+ A+
A+A+
Unique to Springer
Unique to Plectix
Unique to 101668678
T-Cell Development
Cancer Promoting GenesInterleukin-7
(node 1, unique ID) (node 2, unique ID)
< Source concept > < Target Concept > < Relations (edge) >
class date value owner condition Etc.
}
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KNEWCO
Unique to 101668678
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KNEWCO
curatedcuratedcurated
QuickTime™ and a decompressor
are needed to see this picture.
Co-occ
QuickTime™ and a decompressor
are needed to see this picture.
All Triples
Remove
Ambiguity
and
Redundancy
Curated
Observational
Smart Triples
Inferred
Knowledge Space
(node 1, unique ID) (node 2, unique ID)
< Source concept > < Target Concept > < Relations (edge) >
class date value owner condition Etc.
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KNEWCO
Curated databases
•SwissProt•Gene Ontology•NCBO (ontologies)•Peroxisome•InWeb•STRING•HAPMAP•LOVD•Reactome•IHop
Literature (peer reviewed)
•Elsevier•Springer•Wiley•BMC•PubMed•SciELO•PLoS•etc.
‘Grey’ literature
•Blogs •SEED•EURORDIS•UPPMD•(NORD)•SPARC•Research CR•SOUHL
Community-generated
•SIB-lab •PatientsLikeMe •Sermo•Plectix•NBIC•WikiProfessional•WikiPathways•OWW•Alert•BioBanks
Raw data
•GEO•Express•Many NBIC data•Many NGI center data•Many public data.
sell
sustainability
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KNEWCO
Download Concept Web
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)
Private expression data (3000 extra edges, by Merck) (from proprietary data)
InWeb edges (240,000 unique edges from 17 species) (from proprietary data)
Plectix edges (5,000 extra edges (PPI modeling) (from proprietary data)
Gene (co-expression databases (GEO, Express… – 25 square genes) (from public data)
STRING edges (200,000 gene-gene edges) (from semi public 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)
Et Cetera
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KNEWCO
What one can do to make scientific literature What one can do to make scientific literature even more useful: even more useful:
Helping users find what is appropriateHelping users find what is appropriate
What one can do to make scientific literature What one can do to make scientific literature even more useful: even more useful:
Helping users find what is appropriateHelping users find what is appropriate
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KNEWCO
Slide by Carl Lagoze (Cornell) – from this presentation:http://journal.webscience.org/112/3/orechem.pdf
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KNEWCO
Using Knewco’s freely available functionality*, scientific publishers can add semantic functionality to their material by way of highlighting concepts and then linking to additional pertinent information about that concept as well as further search possibilities with automatic expansion of the search argument with synonyms.
*Knewco is a Concept Web Alliance memberButton changes
when clicked
An example ‘mash-up’: On the basis of Semantic Highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Semantic highlighting
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KNEWCO
Concept Web AllianceInaugural Meeting
May 8th, New York Hall of Science
“…an important and critically necessary meeting”
Info: http://conceptweblog.wordpress.comInfo: http://conceptweblog.wordpress.com
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KNEWCO
Demo:Demo:http://demo.knewco.comhttp://demo.knewco.com
Wikimore:Wikimore:http://wikimore.orghttp://wikimore.org
Concept Web:Concept Web:http://conceptweblog.wordpress.comhttp://conceptweblog.wordpress.com
Credits
Thinking Neanderthal man (after Rodin)http://blogs.sundaymercury.net/weirdscience
Needle transporthttp://fisherwy.blogspot.com
Cupped handswww.goldcoast.qld.gov.au
Ship at seahttp://vikingeskibsmuseet.dk
Scientistwww.drugdevelopment-technology.com
Jungle (detail)Henri Rousseau
Jungle (aerial – 2x)http://passporttoknowledge.com
Triples etc.Barend Mons
FinFin