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© Copyright 2011 Digital Enterprise Research Institute. All rights
reserved.
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
From Linked Data to
Networked Knowledge
Stefan Decker
Stefan.Decker@deri.org
http://www.StefanDecker.org/
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Cave Drawings 30000 BC
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Writing: 3200 BC
(Sumerian cuneiform)
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Printing Press
(Gutenberg 1450)
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Photography
(Daguerre 1839)
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Phonograph (Edison 1877)
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Movies (Lumiere 1895)
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Bush’s camera on the
head
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge9
Memex
“A memex is a device
in which an individual stores
all his books, records, and communications,
and which is mechanized so that it may be consulted
with exceeding speed and flexibility”
Posited by Vannevar Bush in “As We May Think”
The Atlantic Monthly, July 1945
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge10
Sketch of memex
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
oNLine System- NLS, 1968
(Doug Engelbart, SRI)
“By ‘augmenting human
intellect’ we mean
increasing the
capability of a man to
approach a complex
problem situation, to
gain comprehension
to suit his particular
needs, and to derive
solutions to
problems.”
The Mouse;
Word Processing;
Data Sharing;
Hypertext;
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
ARPANET (1969)
(John Postel, David Crocker, Vint Cerf)
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Xanadu (Ted Nelson
~1960-???)
13
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
World Wide Web
(Tim Berners-Lee 1989)
WWW (Tim Berners-
Lee)
“There was a second
part of the dream […]
we could then use
computers to help us
analyse it, make sense
of what we re doing,
where we individually fit
in, and how we can
better work together.”
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge15 of 46
Making Progress…
Memex (Vannevar Bush)
A memex is “a device in which an individual
stores all his books, records, and
communications.”
Augmenting Human Intellect
(Doug Engelbart)
“By "augmenting human intellect" we mean
increasing the capability of a man to approach a
complex problem situation, to gain
comprehension to suit his particular needs, and to
derive solutions to problems.”
WWW (Tim Berners-Lee)
“There was a second part of the dream […] we
could then use computers to help us analyse it,
make sense of what we re doing, where we
individually fit in, and how we can better work
together.”
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
A Network of Data
and Knowledge
n  Interconnected
n  Universal
n  All encompassing
n  assists humans,
organisations and systems
with problem solving
n  enabling innovation and
increased productivity
?
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
?
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
1.  Scalability: No growth scalability problem
(e.g., no back links from HTML pages)
2.  No censorship: no lengthy permission or
review process
3.  Positive feedback loop: exploit Metcalf’s
Law
What enabled the Web?
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Metcalfe's law:
The value of a
network is
proportional to the
square of the number
of connected members
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Metcalfe’s Law 1: Links
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Metcalfe’s Law 2
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
1. Scalability. No centralized
infrastructure (e.g., a central object
repository) required.
2. No censorship. It must be possible
to publish data without having to ask
for prior permission.
3. Positive feedback loop. Capitalize on
Metcalfe’s Law.
Requirements for a Data Web
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Enabling Metcalfe’s Law
1.  Global Object Identity.
2.  Composability: The value of data can be increased if it can be combined
with other data. Composability has a number of consequences:
1.  schema-less. ( Combined data originating from difference sources
unlikely to conform to a schema)
2.  self-describing
3.  “object centric”. In order to integrate information about different
entities data must be related to these entities.
4.  graph-based. The composition of multiple object-centric data
sources results in a graph in the general case.
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Observations
•  The relational model does not fulfill these requirements (not
composable, no global object id)
•  XML is not object centric and not composable.
•  Graph based data formats are composable
•  RDF fulfills these requirements.
•  Claim: Any data format that fulfills the requirements is “more or
less” isomorphic to RDF.
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
26 of 46
The usual two
Ingredients
1.  RDF – Resource Description Framework
Graph based Data – nodes and arcs
¨  Identifies objects (URIs)
¨  Interlink information (Relationships)
2.  Vocabularies (Ontologies)
¨  provide shared understanding of a domain
¨  organise knowledge in a machine-comprehensible way
¨  give an exploitable meaning to the data
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Linked Open Data cloud
- domains
Over 200 open data sets with more than 25 billion facts,
interlinked by 400 million typed links, doubling every 10 month!
http://lod-cloud.net/
Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch.
Media
Government
Geo
Publications
User-generated
Life sciences
Cross-domain
US government
UK government
BBC
New York Times
LinkedGeoData
27
BestBuy
Overstock.com
Facebook
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Do we really need
Ontologies?
(as we have them right now)
Provocative?
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Anything wrong with
this picture?
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Wasn’t the Web about
sharing?
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Could modeling not be
easy?
Animal? Mammal? Whale?
Class? Instance?
Argh!!!
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
n  Differentiation in Classes and Instances is difficult:
no single way to abstract the world (observe Upper
Ontology wars…..aehm…discussions!)
n  Choices between Instances and Classes done at
design cause usability issues (different treatment in
applications) (animal-mammal-whale)
n  Ontologies cement power structures (prevent
information sharing)
n  Sharing is only top-down
Issues with Ontologies
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
n  Predecessor: Frame Representation Systems
n  “Prototypes: KRL, RLL, and JOSIE employ prototype
frames to represent information about a typical
instance of a class as opposed to the class itself and
as opposed to actual instances of the class.” [Karp,
1993]
n  AFAIK: Formalisation classes as subsets and
instances as elements [Hayes, 1979].
n  Formalization of Frame Systems (Description Logic)
picked up on [Hayes, 1979] and left out alternatives
How did classes/
instances happen?
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
n  Stefan Decker, Dieter Fensel, Frank van Harmelen,
Ian Horrocks, Sergey Melnik, Michel C. A. Klein,
Jeen Broekstra: Knowledge Representation on the
Web. Description Logics 2000: 89-97
n  OIL -> DAML+OIL -> OWL -> OWL 2.0
Note: How did DL & Ontologies/
Classes happen in the Semantic Web?
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
© A. Lienhard, O. Nierstrasz" 3.35	

Class- vs. Prototype-based
Programming Languages!
Class-based: Prototype-based:
>  No classes, only objects
>  Objects define their own
properties and methods
>  Objects delegate to their
prototype(s)
>  Any object can be the
prototype of another object
Prototype-based languages unify objects and classes
From: A. Lienhard, O. Nierstrasz: Prototype based programming
http://www.slidefinder.net/0/03prototypes/03prototypes/10603817
n  Classes share methods and
define common properties"
n  Inheritance along class chain"
n  Instances have exactly the
properties and behavior
defined by their class"
n  Structure typically cannot be
changed at runtime"
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
> JavaScript,
> Self,
> NewtonScript,
> Omega, Cecil,
Examples
From: A. Lienhard, O. Nierstrasz: Prototype based programming
http://www.slidefinder.net/0/03prototypes/03prototypes/10603817
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
How it could look like:
(Horizontal Information
Sharing)
Enabling Metcalfs Law!
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
You can have
Ontologies as well…
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Object foaf:Agent
weblog URL
twitterID String
Object foaf:Person hasPrototype foaf:Agent
fromSource: http://xmlns.com/foaf/spec/#term_Agent
knows foaf:Agent
age [0…120]
gender {Male, Female}
ishuman yes
Object deri:Stefan hasPrototype foaf:person
fromSource: http://xmlns.com/foaf/spec/#term_Person
weblog http://blog.stefandecker.org
twitterID stefanjdecker
age 44
gender Male
FOAF as Prototypes
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
n  Delegation vs. Copying (deep, shallow)
¨  When to delegate (freshness)
¨  When to copy (access too slow, unsecure, unreliable)
¨  Caching, update strategies?
n  Determining object boundaries (e.g., via a scope-
relationship between URIs). E.g., deri:stefan
isScopeOf deri:address. Automatically possible?
n  Object modification – non monotonicity?
n  Referencing an object (URI & Source!)
n  Specialization: Exact semantics?
Challenges/Design
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
n  Knowledge Representation Constructs
(Specialisation)
n  Logic based Formalisation of Prototypes
n  Reasoning (e.g., with Rules)
n  Complexity
n  Large Scale Storage, Querying
n  Collaboration facilities
Research Agenda
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Get the car out of the mud…
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Linked Open Data cloud
- domains
Over 200 open data sets with more than 25 billion facts,
interlinked by 400 million typed links, doubling every 10 month!
http://lod-cloud.net/
Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch.
Media
Government
Geo
Publications
User-generated
Life sciences
Cross-domain
US government
UK government
BBC
New York Times
LinkedGeoData
43
BestBuy
Overstock.com
Facebook
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Problem Statement
Cisplatin
Cisplatin
Cisplatin:
~ €500 per
injection
High Toxicity
Low Quality of
Life
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Methodology –
Combining Open and Private Data
Uniprot
Entrez Gene
BioMart
KEGG
Pathway
What are the
proteins in the
p53 pathway
What is the
sequence for
those proteins?
What genes
encode for
those proteins?
How to
translate
identifiers?
mirBase
What is the sequence of
those microRNA?
MicroCosm
Targets
What microRNA
target those
genes?
p5317
proteins
7
proteins
155 Genes
817 microRNA
20 000 Genes
Linked Data Filtering
Between 500K and a few billion triples…
Schema is at least 10 tables per dataset!
“Classic data integration = 2 months per data source…
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Networked	
  Data	
  
Management	
  
Abstrac4on,	
  
Reasoning,	
  
Analy4cs	
  
	
  
Visualisa4on,	
  
Collabora4on,	
  
Exploita4on	
  
	
  
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Enabling an
iterative exploration process
Transform
, Integrate
Gather
Explore
Analyse
Understand
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Knowledge Pipeline
•  Global Data
•  Flexible
Integration
Linked Data
•  Liquid Processing
•  Flexible
•  Extensible
Big Data
HADOOP
•  Visualisation
•  Analytics
•  Collaboration
•  Exploitation
Knowledge
Discovery
•  Scalability
•  Parallel
Processing
•  Fast Access
FGCP
Cloud
PaaS
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Example
Find all topics in publications relevant to
“neoplasm” and clinical trials relevant to the
publications topics!
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Workflow
Publications
Find all topics in
publications related
to Neoplasm
(e.g., “Neoplasm
Metastasis”)
Topics
Find all Clinical
Trials related to the
identified topics
Clinical Trials
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
Enabling an
iterative exploration process
Transform,
Integrate
Gather
Explore
Analyse
Understand
Digital Enterprise Research Institute www.deri.ie
Enabling Networked Knowledge
A Network of
Knowledge
n  enabling innovation and
increased productivity
n  Interconnected
n  Universal
n  All encompassing
n  assists humans,
organisations and systems
with problem solving
Linked Data
• Search
• Collaboration
• Text Mining
• Science
• Commercialization`

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ESWC SS 2013 - Monday Keynote Stefan Decker: From Linked Data to Networked Knowledge

  • 1. © Copyright 2011 Digital Enterprise Research Institute. All rights reserved. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge From Linked Data to Networked Knowledge Stefan Decker Stefan.Decker@deri.org http://www.StefanDecker.org/
  • 2. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Cave Drawings 30000 BC
  • 3. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Writing: 3200 BC (Sumerian cuneiform)
  • 4. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Printing Press (Gutenberg 1450)
  • 5. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Photography (Daguerre 1839)
  • 6. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Phonograph (Edison 1877)
  • 7. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Movies (Lumiere 1895)
  • 8. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Bush’s camera on the head
  • 9. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge9 Memex “A memex is a device in which an individual stores all his books, records, and communications, and which is mechanized so that it may be consulted with exceeding speed and flexibility” Posited by Vannevar Bush in “As We May Think” The Atlantic Monthly, July 1945
  • 10. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge10 Sketch of memex
  • 11. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge oNLine System- NLS, 1968 (Doug Engelbart, SRI) “By ‘augmenting human intellect’ we mean increasing the capability of a man to approach a complex problem situation, to gain comprehension to suit his particular needs, and to derive solutions to problems.” The Mouse; Word Processing; Data Sharing; Hypertext;
  • 12. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge ARPANET (1969) (John Postel, David Crocker, Vint Cerf)
  • 13. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Xanadu (Ted Nelson ~1960-???) 13
  • 14. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge World Wide Web (Tim Berners-Lee 1989) WWW (Tim Berners- Lee) “There was a second part of the dream […] we could then use computers to help us analyse it, make sense of what we re doing, where we individually fit in, and how we can better work together.”
  • 15. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge15 of 46 Making Progress… Memex (Vannevar Bush) A memex is “a device in which an individual stores all his books, records, and communications.” Augmenting Human Intellect (Doug Engelbart) “By "augmenting human intellect" we mean increasing the capability of a man to approach a complex problem situation, to gain comprehension to suit his particular needs, and to derive solutions to problems.” WWW (Tim Berners-Lee) “There was a second part of the dream […] we could then use computers to help us analyse it, make sense of what we re doing, where we individually fit in, and how we can better work together.”
  • 16. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge A Network of Data and Knowledge n  Interconnected n  Universal n  All encompassing n  assists humans, organisations and systems with problem solving n  enabling innovation and increased productivity ?
  • 17. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge ?
  • 18. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge 1.  Scalability: No growth scalability problem (e.g., no back links from HTML pages) 2.  No censorship: no lengthy permission or review process 3.  Positive feedback loop: exploit Metcalf’s Law What enabled the Web?
  • 19. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Metcalfe's law: The value of a network is proportional to the square of the number of connected members
  • 20. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Metcalfe’s Law 1: Links
  • 21. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Metcalfe’s Law 2
  • 22. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge
  • 23. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge 1. Scalability. No centralized infrastructure (e.g., a central object repository) required. 2. No censorship. It must be possible to publish data without having to ask for prior permission. 3. Positive feedback loop. Capitalize on Metcalfe’s Law. Requirements for a Data Web
  • 24. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Enabling Metcalfe’s Law 1.  Global Object Identity. 2.  Composability: The value of data can be increased if it can be combined with other data. Composability has a number of consequences: 1.  schema-less. ( Combined data originating from difference sources unlikely to conform to a schema) 2.  self-describing 3.  “object centric”. In order to integrate information about different entities data must be related to these entities. 4.  graph-based. The composition of multiple object-centric data sources results in a graph in the general case.
  • 25. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Observations •  The relational model does not fulfill these requirements (not composable, no global object id) •  XML is not object centric and not composable. •  Graph based data formats are composable •  RDF fulfills these requirements. •  Claim: Any data format that fulfills the requirements is “more or less” isomorphic to RDF.
  • 26. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge 26 of 46 The usual two Ingredients 1.  RDF – Resource Description Framework Graph based Data – nodes and arcs ¨  Identifies objects (URIs) ¨  Interlink information (Relationships) 2.  Vocabularies (Ontologies) ¨  provide shared understanding of a domain ¨  organise knowledge in a machine-comprehensible way ¨  give an exploitable meaning to the data
  • 27. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Linked Open Data cloud - domains Over 200 open data sets with more than 25 billion facts, interlinked by 400 million typed links, doubling every 10 month! http://lod-cloud.net/ Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. Media Government Geo Publications User-generated Life sciences Cross-domain US government UK government BBC New York Times LinkedGeoData 27 BestBuy Overstock.com Facebook
  • 28. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Do we really need Ontologies? (as we have them right now) Provocative?
  • 29. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Anything wrong with this picture?
  • 30. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Wasn’t the Web about sharing?
  • 31. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Could modeling not be easy? Animal? Mammal? Whale? Class? Instance? Argh!!!
  • 32. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge n  Differentiation in Classes and Instances is difficult: no single way to abstract the world (observe Upper Ontology wars…..aehm…discussions!) n  Choices between Instances and Classes done at design cause usability issues (different treatment in applications) (animal-mammal-whale) n  Ontologies cement power structures (prevent information sharing) n  Sharing is only top-down Issues with Ontologies
  • 33. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge n  Predecessor: Frame Representation Systems n  “Prototypes: KRL, RLL, and JOSIE employ prototype frames to represent information about a typical instance of a class as opposed to the class itself and as opposed to actual instances of the class.” [Karp, 1993] n  AFAIK: Formalisation classes as subsets and instances as elements [Hayes, 1979]. n  Formalization of Frame Systems (Description Logic) picked up on [Hayes, 1979] and left out alternatives How did classes/ instances happen?
  • 34. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge n  Stefan Decker, Dieter Fensel, Frank van Harmelen, Ian Horrocks, Sergey Melnik, Michel C. A. Klein, Jeen Broekstra: Knowledge Representation on the Web. Description Logics 2000: 89-97 n  OIL -> DAML+OIL -> OWL -> OWL 2.0 Note: How did DL & Ontologies/ Classes happen in the Semantic Web?
  • 35. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge © A. Lienhard, O. Nierstrasz" 3.35 Class- vs. Prototype-based Programming Languages! Class-based: Prototype-based: >  No classes, only objects >  Objects define their own properties and methods >  Objects delegate to their prototype(s) >  Any object can be the prototype of another object Prototype-based languages unify objects and classes From: A. Lienhard, O. Nierstrasz: Prototype based programming http://www.slidefinder.net/0/03prototypes/03prototypes/10603817 n  Classes share methods and define common properties" n  Inheritance along class chain" n  Instances have exactly the properties and behavior defined by their class" n  Structure typically cannot be changed at runtime"
  • 36. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge > JavaScript, > Self, > NewtonScript, > Omega, Cecil, Examples From: A. Lienhard, O. Nierstrasz: Prototype based programming http://www.slidefinder.net/0/03prototypes/03prototypes/10603817
  • 37. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge How it could look like: (Horizontal Information Sharing) Enabling Metcalfs Law!
  • 38. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge You can have Ontologies as well…
  • 39. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Object foaf:Agent weblog URL twitterID String Object foaf:Person hasPrototype foaf:Agent fromSource: http://xmlns.com/foaf/spec/#term_Agent knows foaf:Agent age [0…120] gender {Male, Female} ishuman yes Object deri:Stefan hasPrototype foaf:person fromSource: http://xmlns.com/foaf/spec/#term_Person weblog http://blog.stefandecker.org twitterID stefanjdecker age 44 gender Male FOAF as Prototypes
  • 40. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge n  Delegation vs. Copying (deep, shallow) ¨  When to delegate (freshness) ¨  When to copy (access too slow, unsecure, unreliable) ¨  Caching, update strategies? n  Determining object boundaries (e.g., via a scope- relationship between URIs). E.g., deri:stefan isScopeOf deri:address. Automatically possible? n  Object modification – non monotonicity? n  Referencing an object (URI & Source!) n  Specialization: Exact semantics? Challenges/Design
  • 41. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge n  Knowledge Representation Constructs (Specialisation) n  Logic based Formalisation of Prototypes n  Reasoning (e.g., with Rules) n  Complexity n  Large Scale Storage, Querying n  Collaboration facilities Research Agenda
  • 42. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Get the car out of the mud…
  • 43. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Linked Open Data cloud - domains Over 200 open data sets with more than 25 billion facts, interlinked by 400 million typed links, doubling every 10 month! http://lod-cloud.net/ Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. Media Government Geo Publications User-generated Life sciences Cross-domain US government UK government BBC New York Times LinkedGeoData 43 BestBuy Overstock.com Facebook
  • 44. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Problem Statement Cisplatin Cisplatin Cisplatin: ~ €500 per injection High Toxicity Low Quality of Life
  • 45. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Methodology – Combining Open and Private Data Uniprot Entrez Gene BioMart KEGG Pathway What are the proteins in the p53 pathway What is the sequence for those proteins? What genes encode for those proteins? How to translate identifiers? mirBase What is the sequence of those microRNA? MicroCosm Targets What microRNA target those genes? p5317 proteins 7 proteins 155 Genes 817 microRNA 20 000 Genes Linked Data Filtering Between 500K and a few billion triples… Schema is at least 10 tables per dataset! “Classic data integration = 2 months per data source…
  • 46. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Networked  Data   Management   Abstrac4on,   Reasoning,   Analy4cs     Visualisa4on,   Collabora4on,   Exploita4on    
  • 47. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Enabling an iterative exploration process Transform , Integrate Gather Explore Analyse Understand
  • 48. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Knowledge Pipeline •  Global Data •  Flexible Integration Linked Data •  Liquid Processing •  Flexible •  Extensible Big Data HADOOP •  Visualisation •  Analytics •  Collaboration •  Exploitation Knowledge Discovery •  Scalability •  Parallel Processing •  Fast Access FGCP Cloud PaaS
  • 49. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Example Find all topics in publications relevant to “neoplasm” and clinical trials relevant to the publications topics!
  • 50. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Workflow Publications Find all topics in publications related to Neoplasm (e.g., “Neoplasm Metastasis”) Topics Find all Clinical Trials related to the identified topics Clinical Trials
  • 51. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge
  • 52. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge Enabling an iterative exploration process Transform, Integrate Gather Explore Analyse Understand
  • 53. Digital Enterprise Research Institute www.deri.ie Enabling Networked Knowledge A Network of Knowledge n  enabling innovation and increased productivity n  Interconnected n  Universal n  All encompassing n  assists humans, organisations and systems with problem solving Linked Data • Search • Collaboration • Text Mining • Science • Commercialization`