Transcript Document

“
Please observe. In the space of one hundred and seventy-six years the
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.
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 Lower Mississippi River was upward of one million three hundred
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
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
have joined their streets together, and be plodding comfortably along
under a single mayor and a mutual board of aldermen. There is
something fascinating about science. One gets such wholesale returns of
conjecture out of such a trifling investment of fact.
”
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Beyond Open Access
Jan Velterop
UKSG, Torquay, March 30, 2009
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“
There is something fascinating about science.
One gets such wholesale returns of conjecture out of
such a trifling investment of fact.
”
Mark Twain, Life on the Mississippi
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What’s wrong?
We have far too few returns in terms of actionable
knowledge out of such overwhelming investment of
fact!
The reason is that a lot of fact is deeply hidden!
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Current Knowledge Transfer
An analogy
Needle transport
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Information overload?
Too much knowledge?
Stop acquiring it?
Just filtering it?
Or organisation underload?
Lack of conceptual structure?
Unprecedented opportunity?
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Information ‘overload’ will increase
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Analogy:
What is the use
of water?
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H2O
Drink
(take in)
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What is the use
of information?
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Age to Know
Read
(take in)
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Publish articles
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Publish articles
obesity
Qu i c k T i m e ™ a n d a
d e c o m p re s s o r
a re n e e d e d to s e e th i s p i c t u re .
body composition
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diabetes
Experienced in
publishing articles
e.g. providing author proofs
with proposed triples and
asking them to verify those
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Living not on detail alone
Getting the big picture – too
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Tools, RDF, OWL, OBO, Protégé
Community
Annotation
(a posteriori)
Community
Annotation
(a posteriori)
Bio
commontology
<ID1><edge><ID2>
Harmonized data
Triplet construction
(unsupervised)
Community
Annotation
(a priori)
Peregrine
Concept Mapping
Direct feed
Blogs, etc.
MRS
Index, virtual concepts
Daily feed
Uniprot
PubMed
Nextprot
CALIPHO
InWeb
WikiPro
SERMO
Information silos
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BioBanks
e.g. LOVD
GEO
GWA
(node 1, unique ID)
(node 2, unique ID)
< Source concept >
class
< Relations (edge) >
date
value
<Type F1> Database facts (multiple attributes)
<Type F2> Community Annotations
owner
}
< Target Concept >
Etc.
condition
F+ C+ A+
<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)
C+ A+
A+
Multiple Triples
T-Cell Development
Unique to 101668678
Graph Building (e.g. WikiPathways)
Cancer Promoting Genes
Interleukin-7
Unique to Springer
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Unique to Plectix
Unique to 101668678
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(node 1, unique ID)
(node 2, unique ID)
< Source concept >
class
< Relations (edge) >
date
All Triples
value
owner
< Target Concept >
condition
Etc.
Smart Triples
curated
curated
curated
Curated
Remove
Co-occ
Ambiguity
Observational
Qu i c k T i m e ™ a n d a
d e c o m p re s s o r
a re n e e d e d t o s e e t h i s p i c t u re .
and
Redundancy
Qu i c k T i m e ™ a n d a
d e c o m p re s s o r
a re n e e d e d t o s e e t h i s p i c t u re .
Inferred
Knowledge Space
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sustainability
sell
Curated databases
Community-generated
‘Grey’ literature
Literature (peer reviewed)
•SwissProt
•Gene Ontology
•NCBO (ontologies)
•Peroxisome
•InWeb
•STRING
•HAPMAP
•LOVD
•Reactome
•IHop
•SIB-lab
•PatientsLikeMe
•Sermo
•Plectix
•NBIC
•WikiProfessional
•WikiPathways
•OWW
•Alert
•BioBanks
•Blogs
•SEED
•EURORDIS
•UPPMD
•(NORD)
•SPARC
•Research CR
•SOUHL
•Elsevier
•Springer
•Wiley
•BMC
•PubMed
•SciELO
•PLoS
•etc.
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Raw data
•GEO
•Express
•Many NBIC data
•Many NGI center data
•Many public data.
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)
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
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What one can do to make scientific literature
even more useful:
Helping users find what is appropriate
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Slide by Carl Lagoze (Cornell) – from this presentation:
http://journal.webscience.org/112/3/orechem.pdf
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An example ‘mash-up’:
On the basis of Semantic Highlighting
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.
Button
changes when
clicked
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*Knewco is a Concept Web Alliance member
Semantic highlighting
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Semantic highlighting
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Semantic highlighting
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Semantic highlighting
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Semantic highlighting
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Semantic highlighting
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Semantic highlighting
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Semantic highlighting
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Semantic highlighting
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Semantic highlighting
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Semantic highlighting
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Semantic highlighting
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Concept Web Alliance
Inaugural Meeting
May 8th, New York Hall of Science
Info: http://conceptweblog.wordpress.com
“…an important and critically necessary meeting”
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http://blogs.sundaymercury.net/weirdscience
Needle transport
http://fisherwy.blogspot.com
Cupped hands
www.goldcoast.qld.gov.au
Ship at sea
http://vikingeskibsmuseet.dk
Fin
Scientist
www.drugdevelopment-technology.com
Jungle (detail)
Henri Rousseau
Jungle (aerial – 2x)
http://passporttoknowledge.com
Triples etc.
Barend Mons
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Demo:
http://demo.knewco.com
Wikimore:
http://wikimore.org
Concept Web:
http://conceptweblog.wordpress.com