Summary of thoughts on data-driven papers and Elsevier Grand Challenges

1. Data-driven Papers and
Grand Challenges
Anita de Waard, a.dewaard@elsevier.com
Disruptive Technologies Director, Elsevier Labs
August 26, 2010

2. Science is made of information...

3. Science is made of information...
...that gets created...

4. Science is made of information...
...that gets created... ... and destroyed.

5. What is the problem?

6. What is the problem?
1. Researchers can’t keep track of their data.

7. What is the problem?
1. Researchers can’t keep track of their data.
2. Data is not stored in a way that is easy for authors.

8. What is the problem?
1. Researchers can’t keep track of their data.
2. Data is not stored in a way that is easy for authors.
3. For readers, article text is not linked to the underlying data.

9. The Vision Work done with Ed Hovy, Phil Bourne,
Gully Burns and Cartic Ramakrishnan

10. The Vision Work done with Ed Hovy, Phil Bourne,
Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata
metadata (including provenance) and relations to other data items
metadata added to it.
metadata
metadata
metadata

11. The Vision Work done with Ed Hovy, Phil Bourne,
Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata
metadata (including provenance) and relations to other data items
metadata added to it.
2. Workflow: All data items created in the lab are added
metadata
to a (lab-owned) workflow system.
metadata
metadata

12. The Vision Work done with Ed Hovy, Phil Bourne,
Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata
metadata (including provenance) and relations to other data items
metadata added to it.
2. Workflow: All data items created in the lab are added
metadata
to a (lab-owned) workflow system.
3. Authoring: A paper is written in an authoring tool which
can pull data with provenance from the workflow tool in the
appropriate representation into the document.
metadata
metadata
Rats were subjected to two
grueling tests
(click on fig 2 to see underlying
data). These results suggest that
the neurological pain pro-

13. The Vision Work done with Ed Hovy, Phil Bourne,
Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata
metadata (including provenance) and relations to other data items
metadata added to it.
2. Workflow: All data items created in the lab are added
metadata
to a (lab-owned) workflow system.
3. Authoring: A paper is written in an authoring tool which
can pull data with provenance from the workflow tool in the
appropriate representation into the document.
metadata 4. Editing and review: Once the co-authors agree, the
paper is ‘exposed’ to the editors, who in turn expose it to
metadata reviewers. Reports are stored in the authoring/editing
system, the paper gets updated, until it is validated.
Rats were subjected to two
grueling tests
(click on fig 2 to see underlying
data). These results suggest that
the neurological pain pro-
Review
Revise
Edit

14. The Vision Work done with Ed Hovy, Phil Bourne,
Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata
metadata (including provenance) and relations to other data items
metadata added to it.
2. Workflow: All data items created in the lab are added
metadata
to a (lab-owned) workflow system.
3. Authoring: A paper is written in an authoring tool which
can pull data with provenance from the workflow tool in the
appropriate representation into the document.
metadata 4. Editing and review: Once the co-authors agree, the
paper is ‘exposed’ to the editors, who in turn expose it to
metadata reviewers. Reports are stored in the authoring/editing
system, the paper gets updated, until it is validated.
5. Publishing and distribution: When a paper is
published, a collection of validated information is
exposed to the world. It remains connected to its related
Rats were subjected to two
data item, and its heritage can be traced.
grueling tests
(click on fig 2 to see underlying
data). These results suggest that
the neurological pain pro-
Review
Revise
Edit

15. The Vision Work done with Ed Hovy, Phil Bourne,
Gully Burns and Cartic Ramakrishnan
1. Research: Each item in the system has metadata
metadata (including provenance) and relations to other data items
metadata added to it.
2. Workflow: All data items created in the lab are added
metadata
to a (lab-owned) workflow system.
3. Authoring: A paper is written in an authoring tool which
can pull data with provenance from the workflow tool in the
appropriate representation into the document.
metadata 4. Editing and review: Once the co-authors agree, the
paper is ‘exposed’ to the editors, who in turn expose it to
metadata reviewers. Reports are stored in the authoring/editing
system, the paper gets updated, until it is validated.
5. Publishing and distribution: When a paper is
published, a collection of validated information is
exposed to the world. It remains connected to its related
Rats were subjected to two
data item, and its heritage can be traced.
grueling tests
(click on fig 2 to see underlying
6. User applications: distributed applications run on this
data). These results suggest that ‘exposed data’ universe.
the neurological pain pro-
Some other publisher
Review
Revise
Edit

16. What is needed to get there?

17. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly

18. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly
Authoring and reviewing tools: that enable use of rich and
provenance-tracked elements

19. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly
Authoring and reviewing tools: that enable use of rich and
provenance-tracked elements
Metadata standards: Standards that allow exchange of
information on any knowledge item created in a lab,
including provenance/privacy/IPR rights

20. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly
Authoring and reviewing tools: that enable use of rich and
provenance-tracked elements
Metadata standards: Standards that allow exchange of
information on any knowledge item created in a lab,
including provenance/privacy/IPR rights
Semantic/Linked Data XML repositories.

21. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly
Authoring and reviewing tools: that enable use of rich and
provenance-tracked elements
Metadata standards: Standards that allow exchange of
information on any knowledge item created in a lab,
including provenance/privacy/IPR rights
Semantic/Linked Data XML repositories.
Publishing systems that are application servers

22. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly
Authoring and reviewing tools: that enable use of rich and
provenance-tracked elements
Metadata standards: Standards that allow exchange of
information on any knowledge item created in a lab,
including provenance/privacy/IPR rights
Semantic/Linked Data XML repositories.
Publishing systems that are application servers
Social change: Scientists store, track and annotate their
work.

23. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly tool builders
Authoring and reviewing tools: that enable use of rich and
provenance-tracked elements
Metadata standards: Standards that allow exchange of
information on any knowledge item created in a lab,
including provenance/privacy/IPR rights
Semantic/Linked Data XML repositories.
Publishing systems that are application servers
Social change: Scientists store, track and annotate their
work.

24. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly tool builders
Authoring and reviewing tools: that enable use of rich and
provenance-tracked elements tool builders
Metadata standards: Standards that allow exchange of
information on any knowledge item created in a lab,
including provenance/privacy/IPR rights
Semantic/Linked Data XML repositories.
Publishing systems that are application servers
Social change: Scientists store, track and annotate their
work.

25. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly tool builders
Authoring and reviewing tools: that enable use of rich and
provenance-tracked elements tool builders
Metadata standards: Standards that allow exchange of
information on any knowledge item created in a lab,
including provenance/privacy/IPR rights standards bodies
Semantic/Linked Data XML repositories.
Publishing systems that are application servers
Social change: Scientists store, track and annotate their
work.

26. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly tool builders
Authoring and reviewing tools: that enable use of rich and
provenance-tracked elements tool builders
Metadata standards: Standards that allow exchange of
information on any knowledge item created in a lab,
including provenance/privacy/IPR rights standards bodies
Semantic/Linked Data XML repositories. publishers
Publishing systems that are application servers
Social change: Scientists store, track and annotate their
work.

27. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly tool builders
Authoring and reviewing tools: that enable use of rich and
provenance-tracked elements tool builders
Metadata standards: Standards that allow exchange of
information on any knowledge item created in a lab,
including provenance/privacy/IPR rights standards bodies
Semantic/Linked Data XML repositories. publishers
Publishing systems that are application servers publishers
Social change: Scientists store, track and annotate their
work.

28. What is needed to get there?
Workflow tools: Linked-data-based workflow tools for all
sciences: scalable, safe, and user-friendly tool builders
Authoring and reviewing tools: that enable use of rich and
provenance-tracked elements tool builders
Metadata standards: Standards that allow exchange of
information on any knowledge item created in a lab,
including provenance/privacy/IPR rights standards bodies
Semantic/Linked Data XML repositories. publishers
Publishing systems that are application servers publishers
Social change: Scientists store, track and annotate their
work. institutes, funding bodies, individuals

29. A. Workflow tools are emerging

30. A. Workflow tools are emerging
http://MyExperiment.org

31. A. Workflow tools are emerging
http://VisTrails.org
http://MyExperiment.org

32. A. Workflow tools are emerging
http://VisTrails.org
http://MyExperiment.org
http://wings.isi.edu/

33. B. Authoring ‘ecosystems’: e.g., SWAN
SWAN Semantic Relationships
Excel file describes
Private makes hasEvidence annotates
comment
publication person
Claim
hasEvidence authoredBy authorOf
publication
shareWith
describes
MSWORD file Slide by Tim Clark

34. B. Authoring ‘ecosystems’: e.g., SWAN
person SWAN Semantic Relationships
annotates
comment
authoredBy
makes hasEvidence
concept
annotates
Claim publication
shareWith hypothesis
makes hasEvidence
gene
Claim publication
hasEvidence discussedIn
group
publication
Public Excel file describes describes
PDFs
Private makes hasEvidence annotates
comment
publication person
Claim
hasEvidence authoredBy authorOf
publication
shareWith
describes
MSWORD file Slide by Tim Clark

35. C. Example of Metadata: Harvard’s Annotation
foaf:person rdf:Type Ontology
http://www.ht.org/
foaf.rdf#me
June 1, 2010
pav:createdBy
pav:createdOn ann:annotates http://anyurl.com/sf_pat01.html
hasTag
rdf:Type
hasTopic
Tag
Atomic
tag
FMA:skull ann:context
onDocument
Linear skull fracture
rdf:Type
Other annotations on the same document:
1. Atomic annotation on image (tag: “hematoma”)
2. General annotation (tag: “injury”) InitEndCornerSelector
init
Other annotations on similar documents: (304, 507)
1. General annotation (tag: “skull fracture”) rdfs:SubClassOf
end
(380, 618)
ImageSelector
Slide by Tim Clark

36. D. Linked Data at Elsevier

37. D. Linked Data at Elsevier
<ce:section id=#123>

38. D. Linked Data at Elsevier
this says
<ce:section id=#123> mice like cheese

39. D. Linked Data at Elsevier
said @anita
on May 31 2010
this says
<ce:section id=#123> mice like cheese

40. D. Linked Data at Elsevier
but we all know
she was jetlagged then
said @anita
on May 31 2010
this says
<ce:section id=#123> mice like cheese

41. D. Linked Data at Elsevier
immutable, $$, proprietary
but we all know
she was jetlagged then
said @anita
on May 31 2010
this says
<ce:section id=#123> mice like cheese

42. D. Linked Data at Elsevier
immutable, $$, proprietary dynamic, personal, task-driven, - open?
but we all know
she was jetlagged then
said @anita
on May 31 2010
this says
<ce:section id=#123> mice like cheese

43. E. ScienceDirect Application Server

44. F. Social Change. Some next Steps:

45. F. Social Change. Some next Steps:
• 2010 - 2011: Try to gather resources, current leaders, etc. for
‘Future of Research Communication’ effort

46. F. Social Change. Some next Steps:
• 2010 - 2011: Try to gather resources, current leaders, etc. for
‘Future of Research Communication’ effort
–Fall 2010: Develop virtual community (with Harvard)

47. F. Social Change. Some next Steps:
• 2010 - 2011: Try to gather resources, current leaders, etc. for
‘Future of Research Communication’ effort
–Fall 2010: Develop virtual community (with Harvard)
–August 2011: Dagstuhl Workshop:

48. F. Social Change. Some next Steps:
• 2010 - 2011: Try to gather resources, current leaders, etc. for
‘Future of Research Communication’ effort
–Fall 2010: Develop virtual community (with Harvard)
–August 2011: Dagstuhl Workshop:
• Involve key people (include funding bodies, libraries,
institutions) to see where bottlenecks are

49. F. Social Change. Some next Steps:
• 2010 - 2011: Try to gather resources, current leaders, etc. for
‘Future of Research Communication’ effort
–Fall 2010: Develop virtual community (with Harvard)
–August 2011: Dagstuhl Workshop:
• Involve key people (include funding bodies, libraries,
institutions) to see where bottlenecks are
• Write white paper, implement

50. F. Social Change. Some next Steps:
• 2010 - 2011: Try to gather resources, current leaders, etc. for
‘Future of Research Communication’ effort
–Fall 2010: Develop virtual community (with Harvard)
–August 2011: Dagstuhl Workshop:
• Involve key people (include funding bodies, libraries,
institutions) to see where bottlenecks are
• Write white paper, implement
• 2011: ICCS ‘Executable Paper Challenge’?

52. Scope: Tools and processes to:
- Improve the process of creating, reviewing and
editing scientific content
- Interpret, visualize or connect science knowledge
- Provide tools/ideas for measuring the impact of these
improvements.

53. Scope: Tools and processes to:
- Improve the process of creating, reviewing and
editing scientific content
- Interpret, visualize or connect science knowledge
- Provide tools/ideas for measuring the impact of these
improvements.
June 2008: 71 Submissions from 15 countries.

54. Scope: Tools and processes to:
- Improve the process of creating, reviewing and
editing scientific content
- Interpret, visualize or connect science knowledge
- Provide tools/ideas for measuring the impact of these
improvements.
June 2008: 71 Submissions from 15 countries.
August 2008: 10 Semi-finalists teams, access to:
- 500,000 full text articles
- Plus EMTREE, EmBase, Scopus
- Created tool/demo
- Presented to the Judges
- Wrote a paper (accepted for JWeb Semantics)

55. Scope: Tools and processes to:
- Improve the process of creating, reviewing and
editing scientific content
- Interpret, visualize or connect science knowledge
- Provide tools/ideas for measuring the impact of these
improvements.
June 2008: 71 Submissions from 15 countries.
August 2008: 10 Semi-finalists teams, access to:
- 500,000 full text articles
- Plus EMTREE, EmBase, Scopus
- Created tool/demo
- Presented to the Judges
- Wrote a paper (accepted for JWeb Semantics)
April 2009: Judges selected 4 Finalist teams.

56. Scope: Tools and processes to:
- Improve the process of creating, reviewing and
editing scientific content
- Interpret, visualize or connect science knowledge
- Provide tools/ideas for measuring the impact of these
improvements.
June 2008: 71 Submissions from 15 countries.
August 2008: 10 Semi-finalists teams, access to:
- 500,000 full text articles
- Plus EMTREE, EmBase, Scopus
- Created tool/demo
- Presented to the Judges
- Wrote a paper (accepted for JWeb Semantics)
April 2009: Judges selected 4 Finalist teams.
And the winners were:

57. Scope: Tools and processes to:
- Improve the process of creating, reviewing and
editing scientific content
- Interpret, visualize or connect science knowledge
- Provide tools/ideas for measuring the impact of these
improvements.
June 2008: 71 Submissions from 15 countries.
August 2008: 10 Semi-finalists teams, access to:
- 500,000 full text articles
- Plus EMTREE, EmBase, Scopus
- Created tool/demo
- Presented to the Judges
- Wrote a paper (accepted for JWeb Semantics)
April 2009: Judges selected 4 Finalist teams.
And the winners were:

58. Scope: Tools and processes to:
- Improve the process of creating, reviewing and
editing scientific content
- Interpret, visualize or connect science knowledge
- Provide tools/ideas for measuring the impact of these
improvements.
June 2008: 71 Submissions from 15 countries.
August 2008: 10 Semi-finalists teams, access to:
- 500,000 full text articles
- Plus EMTREE, EmBase, Scopus
- Created tool/demo
- Presented to the Judges
- Wrote a paper (accepted for JWeb Semantics)
April 2009: Judges selected 4 Finalist teams.
And the winners were: