Talk on September 13, at Biocreative III in Bethesda, MD

1. What is inside our full-text articles,
and how do we improve access to it?
Or: Stories, that persuade with data.
Biocreative III Publishers Panel
September 13, 2010
Anita de Waard, a.dewaard@elsevier.com
Disruptive Technologies Director, Elsevier Labs

2. Model of a paper: “Scientific articles are stories...
The Story of Goldilocks Story Grammar Paper The AXH Domain of Ataxin-1 Mediates
and the Three Bears Neurodegeneration through Its Interaction with Gfi-1/
Senseless Proteins
Once upon a time Time Setting Background The mechanisms mediating SCA1 pathogenesis are still not fully
understood, but some general principles have emerged.
a little girl named Goldilocks Characters Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
She went for a walk in the Location Experimental studied and compared in vivo effects and interactions to those of
forest. Pretty soon, she came setup the human protein
upon a house.
She knocked and, when no one Goal Theme Research Gain insight into how Atx-1's function contributes to SCA1
answered, goal pathogenesis. How these interactions might contribute to the
disease process and how they might cause toxicity in only a subse
she walked right in. of neurons play a role in the regulation of gene expression
Atx-1 may in SCA1 is not fully understood.
Attempt Hypothesis
At the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When
were three bowls of porridge. Overexpressed in Files
Goldilocks was hungry. Subgoal Subgoal test the function of the AXH domain
She tasted the porridge from Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand
the first bowl. and Perrimon, 1993) and compared its effects to those of hAtx-1.
This porridge is too hot! she Outcome Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drive
exclaimed. expression in the differentiated R1-R6 photoreceptor cells
(Mollereau et al., 2000 and O'Tousa et al., 1985), results in
neurodegeneration in the eye, as does overexpression of hAtx-1
[82Q]. Although at 2 days after eclosion, overexpression of either
So, she tasted the porridge Activity Data (data not shown),
Atx-1 does not show obvious morphological changes in the
from the second bowl. photoreceptor cells
This porridge is too cold, she Outcome Results both genotypes show many large holes and loss of cell integrity at
said 28 days
So, she tasted the last bowl of Activity Data (Figures 1B-1D).
porridge.
Ahhh, this porridge is just right, Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induce
she said happily and eye abnormalities. The external structures of the eyes that
2 overexpress dAtx-1 show disorganized ommatidia and loss of
she ate it all up. Data interommatidial bristles
(Figure 1F),

3. Model of a paper: “Scientific articles are stories...
The Story of Goldilocks Story Grammar Paper The AXH Domain of Ataxin-1 Mediates
and the Three Bears Neurodegeneration through Its Interaction with Gfi-1/
Senseless Proteins
Once upon a time Time Setting Background The mechanisms mediating SCA1 pathogenesis are still not fully
understood, but some general principles have emerged.
a little girl named Goldilocks Characters Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
She went for a walk in the Location Experimental studied and compared in vivo effects and interactions to those of
forest. Pretty soon, she came setup the human protein
upon a house.
She knocked and, when no one Goal Theme Research Gain insight into how Atx-1's function contributes to SCA1
answered, goal pathogenesis. How these interactions might contribute to the
disease process and how they might cause toxicity in only a subse
she walked right in. of neurons play a role in the regulation of gene expression
Atx-1 may in SCA1 is not fully understood.
Attempt Hypothesis
At the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When
were three bowls of porridge. Overexpressed in Files
Goldilocks was hungry. Subgoal Subgoal test the function of the AXH domain
She tasted the porridge from Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand
the first bowl. and Perrimon, 1993) and compared its effects to those of hAtx-1.
This porridge is too hot! she Outcome Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drive
exclaimed. expression in the differentiated R1-R6 photoreceptor cells
(Mollereau et al., 2000 and O'Tousa et al., 1985), results in
neurodegeneration in the eye, as does overexpression of hAtx-1
[82Q]. Although at 2 days after eclosion, overexpression of either
So, she tasted the porridge Activity Data (data not shown),
Atx-1 does not show obvious morphological changes in the
from the second bowl. photoreceptor cells
This porridge is too cold, she Outcome Results both genotypes show many large holes and loss of cell integrity at
said 28 days
So, she tasted the last bowl of Activity Data (Figures 1B-1D).
porridge.
Ahhh, this porridge is just right, Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induce
she said happily and eye abnormalities. The external structures of the eyes that
2 overexpress dAtx-1 show disorganized ommatidia and loss of
she ate it all up. Data interommatidial bristles
(Figure 1F),

4. “...that persuade (editors/authors/readers!)...”
3

5. “...that persuade (editors/authors/readers!)...”
Aristotle Quintilian Scientific Paper
The introduction of a speech, where one announces the
Introduction subject and purpose of the discourse, and where one usually Introduction:
prooimion / exordium employs the persuasive appeal to ethos in order to positioning
establish credibility with the audience.
Statement of The speaker here provides a narrative account of what has Introduction: research
prothesis Facts/narratio happened and generally explains the nature of the case. question
Summary/ The propositio provides a brief summary of what one is about
propostitio to speak on, or concisely puts forth the charges or accusation. Summary of contents
The main body of the speech where one offers logical
Proof/
pistis confirmatio
arguments as proof. The appeal to logos is emphasized Results
here.
Refutation/ As the name connotes, this section of a speech was devoted to
refutatio answering the counterarguments of one's opponent. Related Work
Following the refutatio and concluding the classical oration, the
Discussion: summary,
epilogos peroratio peroratio conventionally employed appeals through
3 pathos, and often included a summing up. implications.

6. “...that persuade (editors/authors/readers!)...”
Aristotle Quintilian Scientific Paper
The introduction of a speech, where one announces the
Introduction subject and purpose of the discourse, and where one usually Introduction:
prooimion / exordium employs the persuasive appeal to ethos in order to positioning
establish credibility with the audience.
Statement of The speaker here provides a narrative account of what has Introduction: research
prothesis Facts/narratio happened and generally explains the nature of the case. question
Summary/ The propositio provides a brief summary of what one is about
propostitio to speak on, or concisely puts forth the charges or accusation. Summary of contents
The main body of the speech where one offers logical
Proof/
pistis confirmatio
arguments as proof. The appeal to logos is emphasized Results
here.
Refutation/ As the name connotes, this section of a speech was devoted to
refutatio answering the counterarguments of one's opponent. Related Work
Following the refutatio and concluding the classical oration, the
Discussion: summary,
epilogos peroratio peroratio conventionally employed appeals through
3 pathos, and often included a summing up. implications.

7. “... with data.”
4

8. “... with data.”
4

9. “... with data.”
4

10. So how do we improve access to these?
5

11. So how do we improve access to these?
1.1. Better access to ‘story’ elements:
5

12. So how do we improve access to these?
1.1. Better access to ‘story’ elements:
• Learn from Fairy Tale annotation/Proppian Markup?
5

13. So how do we improve access to these?
1.1. Better access to ‘story’ elements:
• Learn from Fairy Tale annotation/Proppian Markup?
5

14. So how do we improve access to these?
1.1. Better access to ‘story’ elements:
• Learn from Fairy Tale annotation/Proppian Markup?
5

15. So how do we improve access to these?
1.1. Better access to ‘story’ elements:
• Learn from Fairy Tale annotation/Proppian Markup?
• W3C HCLS SiG Scientific discourse structure:
5

16. So how do we improve access to these?
1.1. Better access to ‘story’ elements:
• Learn from Fairy Tale annotation/Proppian Markup?
• W3C HCLS SiG Scientific discourse structure:
5

17. 1.2. Element access through Linked Data:

18. 1.2. Element access through Linked Data:
<ce:section id=#123>

19. 1.2. Element access through Linked Data:
this says
<ce:section id=#123> mice like cheese

20. 1.2. Element access through Linked Data:
said @anita
on September 8, 2010
this says
<ce:section id=#123> mice like cheese

21. 1.2. Element access through Linked Data:
but we all know
she was wrong then
said @anita
on September 8, 2010
this says
<ce:section id=#123> mice like cheese

22. 1.2. Element access through Linked Data:
the xml is fixed, but the structure is open!
but we all know
she was wrong then
said @anita
on September 8, 2010
this says
<ce:section id=#123> mice like cheese

23. 1.2. Element access through Linked Data:
the xml is fixed, but the structure is open! allows for layers of annotation
but we all know
she was wrong then
said @anita
on September 8, 2010
this says
<ce:section id=#123> mice like cheese

24. 2.1. Improve access to persuasive elements:
Identify key rhetorical elements in scientific text:
Both seminomas and the EC component of
nonseminomas share features with ES cells. To
exclude that the detection of miR-371-3 merely
reflects its expression pattern in ES cells, we tested
by RPA miR-302a-d, another ES cells-specific
miRNA cluster (Suh et al, 2004). In many of the
miR-371-3 expressing seminomas and
nonseminomas, miR-302a-d was undetectable (Figs
S7 and S8), suggesting that miR-371-3 expression
is a selective event during tumorigenesis.
7

25. 2.1. Improve access to persuasive elements:
Identify key rhetorical elements in scientific text:
Both seminomas and the EC component of
Both seminomas and the EC component of
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
tumorigenesis.
7

26. 2.1. Improve access to persuasive elements:
Identify key rhetorical elements in scientific text:
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
tumorigenesis.
7

27. 2.1. Improve access to persuasive elements:
Identify key rhetorical elements in scientific text:
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
tumorigenesis.
7

28. 2.1. Improve access to persuasive elements:
Identify key rhetorical elements in scientific text:
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
tumorigenesis.
7

29. 2.1. Improve access to persuasive elements:
Identify key rhetorical elements in scientific text:
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
tumorigenesis.
7

30. 2.1. Improve access to persuasive elements:
Identify key rhetorical elements in scientific text:
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
Implication
tumorigenesis.
7

31. 2.1. Improve access to persuasive elements:
Identify key rhetorical elements in scientific text:
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the Goal
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that
miR-371-3 expression is a selective event during
Implication
tumorigenesis.
7

32. 2.1. Improve access to persuasive elements:
Identify key rhetorical elements in scientific text:
Both seminomas and the EC component of
Both seminomas and the EC component of Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the Goal
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that Reg-Implication
miR-371-3 expression is a selective event during
Implication
tumorigenesis.
7

33. 2.1. Improve access to persuasive elements:
Identify key rhetorical elements in scientific text:
Conceptual
Both seminomas and the EC component of
Both seminomas and the EC component of knowledge
Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the Goal
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that Reg-Implication
miR-371-3 expression is a selective event during
Implication
tumorigenesis.
7

34. 2.1. Improve access to persuasive elements:
Identify key rhetorical elements in scientific text:
Conceptual
Both seminomas and the EC component of
Both seminomas and the EC component of knowledge
Fact
nonseminomas share features with ES cells.
nonseminomas share features with ES cells. To
exclude thatthat detection of miR-371-3 merely
To exclude the Goal
reflects its expression pattern in ES cells,reflects its
the detection of miR-371-3 merely we tested Hypothesis
by RPA miR-302a-d, another ES cells-specific
expression pattern in ES cells,
miRNA cluster RPA miR-302a-d, another ES cells-
we tested by (Suh et al, 2004). In many of the
m i R - 3 7 miRNAx p r e s s(Suh et e m2004). a s a n d
specific 1 - 3 e cluster i n g s al, i n o m Method
Experimental
nonseminomas, miR-302a-d was undetectable (Figs
In many of the miR-371-3 expressing seminomas
Evidence
S7 and S8), suggesting that miR-371-3undetectable
and nonseminomas, miR-302a-d was expression Result
is a selective event during tumorigenesis.
(Figs S7 and S8),
suggesting that Reg-Implication
miR-371-3 expression is a selective event during
Implication
tumorigenesis.
7

35. 2.2. Realms in experimental discourse

36. 2.2. Realms in experimental discourse
(1) Both seminomas (2) b. the detection of
and the EC component miR-371-3 merely
of nonseminomas share reflects its expression
features with ES cells. pattern in ES cells,

37. 2.2. Realms in experimental discourse
(1) Both seminomas (2) b. the detection of
and the EC component miR-371-3 merely
of nonseminomas share reflects its expression
features with ES cells. pattern in ES cells,
(2) a. To exclude that

38. 2.2. Realms in experimental discourse
(1) Both seminomas (2) b. the detection of
and the EC component miR-371-3 merely
of nonseminomas share reflects its expression
features with ES cells. pattern in ES cells,
(2) a. To exclude that
(2) c. we tested by RPA (3) a. In many of the miR-371-3
miR-302a-d, another ES expressing seminomas and
cells-specific miRNA cluster nonseminomas, miR-302a-d was
(Suh et al, 2004). undetectable (Figs S7 and S8),

39. 2.2. Realms in experimental discourse
(1) Both seminomas (2) b. the detection of
and the EC component miR-371-3 merely
of nonseminomas share reflects its expression
features with ES cells. pattern in ES cells,
(2) a. To exclude that (3) b. suggesting that
(2) c. we tested by RPA (3) a. In many of the miR-371-3
miR-302a-d, another ES expressing seminomas and
cells-specific miRNA cluster nonseminomas, miR-302a-d was
(Suh et al, 2004). undetectable (Figs S7 and S8),

40. 2.2. Realms in experimental discourse
(1) Both seminomas (2) b. the detection of (3) c. miR-371-3
and the EC component miR-371-3 merely expression is a
of nonseminomas share reflects its expression selective event during
features with ES cells. pattern in ES cells, tumorigenesis.
(2) a. To exclude that (3) b. suggesting that
(2) c. we tested by RPA (3) a. In many of the miR-371-3
miR-302a-d, another ES expressing seminomas and
cells-specific miRNA cluster nonseminomas, miR-302a-d was
(Suh et al, 2004). undetectable (Figs S7 and S8),

41. 2.2. Realms in experimental discourse
Concepts, models, ‘facts’
(1) Both seminomas (2) b. the detection of (3) c. miR-371-3
and the EC component miR-371-3 merely expression is a
of nonseminomas share reflects its expression selective event during
features with ES cells. pattern in ES cells, tumorigenesis.
(2) a. To exclude that (3) b. suggesting that
(2) c. we tested by RPA (3) a. In many of the miR-371-3
miR-302a-d, another ES expressing seminomas and
cells-specific miRNA cluster nonseminomas, miR-302a-d was
(Suh et al, 2004). undetectable (Figs S7 and S8),

42. 2.2. Realms in experimental discourse
Concepts, models, ‘facts’
(1) Both seminomas (2) b. the detection of (3) c. miR-371-3
and the EC component miR-371-3 merely expression is a
of nonseminomas share reflects its expression selective event during
features with ES cells. pattern in ES cells, tumorigenesis.
(2) a. To exclude that (3) b. suggesting that
(2) c. we tested by RPA (3) a. In many of the miR-371-3
miR-302a-d, another ES expressing seminomas and
cells-specific miRNA cluster nonseminomas, miR-302a-d was
(Suh et al, 2004). undetectable (Figs S7 and S8),
Experiment

43. 2.2. Realms in experimental discourse
Concepts, models, ‘facts’
(1) Both seminomas (2) b. the detection of (3) c. miR-371-3
and the EC component miR-371-3 merely expression is a
of nonseminomas share reflects its expression selective event during
features with ES cells. pattern in ES cells, tumorigenesis.
(2) a. To exclude that Transitions (3) b. suggesting that
(2) c. we tested by RPA (3) a. In many of the miR-371-3
miR-302a-d, another ES expressing seminomas and
cells-specific miRNA cluster nonseminomas, miR-302a-d was
(Suh et al, 2004). undetectable (Figs S7 and S8),
Experiment

44. 2.3. Hypotheses, Evidence and Relationships:
9

45. 2.3. Hypotheses, Evidence and Relationships:
9

46. 2.3. Hypotheses, Evidence and Relationships:
9

47. 2.3. Hypotheses, Evidence and Relationships:
9

48. 2.3. Hypotheses, Evidence and Relationships:
9

49. 2.3. Hypotheses, Evidence and Relationships:
Hypothesis 22: Intramembrenous Aβ dimer may be toxic.
Derived from: POSTAT_CONTRIBUTION(This essay explores the possibility that a
fraction of these Abeta peptides never leave the membrane lipid bilayer after they are
generated, but instead exert their toxic effects by competing with and compromising
the functions of intramembranous segments of membrane-bound proteins that serve
many critical functions.
9

50. 2.3. Hypotheses, Evidence and Relationships:
9

51. 2.3. Hypotheses, Evidence and Relationships:
• Collective of groups working on representing scientific text as
– discourse elements
– linked by rhetorical relationships
– connected to data
9

52. 2.3. Hypotheses, Evidence and Relationships:
• Collective of groups working on representing scientific text as
– discourse elements
– linked by rhetorical relationships
– connected to data
• Current efforts:
– W3C HCLS SiG: development of a Rhetorical Document Structure
– Unification of ScholOnto, CiTO, SWAN, SALT relations
9

53. 2.3. Hypotheses, Evidence and Relationships:
• Collective of groups working on representing scientific text as
– discourse elements
– linked by rhetorical relationships
– connected to data
• Current efforts:
– W3C HCLS SiG: development of a Rhetorical Document Structure
– Unification of ScholOnto, CiTO, SWAN, SALT relations
• Developing an Annotation Framework with Harvard/MGH:
– Access to collection of full-text content on Alzheimer’s
– Allow standoff annotation through Harvard’s Annotation Ontology
– Run several hypothesis/event identification tools - access through
U-Compare, UMIA, SciKnowMine
– Allow layering of annotations
– Test with users in Alzheimer community!
9

54. 2.4. Three dimensions of annotation:
measure

55. 2.4. Three dimensions of annotation:
measure

56. 2.4. Three dimensions of annotation:
Granularity
collection
document
claim
triple
entity
measure

57. 2.4. Three dimensions of annotation:
Granularity
collection
document
claim
triple
entity
measure
Means manual
semi-automated
automated

58. 2.4. Three dimensions of annotation:
Granularity
collection
document
claim
triple
entity Mome
measure author/editor typesetter/production reader/curator/data m
Means manual
semi-automated
automated

59. 2.4. Three dimensions of annotation:
Granularity
collection
document
claim
triple
entity Mome
measure author/editor typesetter/production reader/curator/data m
Means manual Entity Markup
semi-automated
automated

60. 2.4. Three dimensions of annotation:
Granularity
collection
document
claim
triple Hypothesis markup
entity Mome
measure author/editor typesetter/production reader/curator/data m
Means manual Entity Markup
semi-automated
automated

61. 2.4. Three dimensions of annotation:
Granularity
collection
document
claim
triple Hypothesis markup
entity Mome
measure author/editor typesetter/production reader/curator/data m
Means manual Entity Markup
semi-automated
automated

62. 3.1. Research data

63. 3.1. Research data
... gets created...

64. 3.1. Research data
... gets created... ... and destroyed!

65. 3.2. Data-driven papers? Work done with Ed Hovy, Phil Bourne,
Gully Burns and Cartic Ramakrishnan

66. 3.2. Data-driven papers? 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

67. 3.2. Data-driven papers? 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

68. 3.2. Data-driven papers? 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-

69. 3.2. Data-driven papers? 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

70. 3.2. Data-driven papers? 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

71. 3.2. Data-driven papers? 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

72. 3.3. Small step: ScienceDirect app store

73. 3.4. Social Change! Some next steps:

74. 3.4. Social Change! Some next steps:

75. 3.4. Social Change! Some next steps:
• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne:
linking data to papers; develop virtual community around
that

76. 3.4. Social Change! Some next steps:
• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne:
linking data to papers; develop virtual community around
that
• June 2011: ‘Executable Paper Challenge’ @ ICCS:
ask computer scientists to submit ideas for ‘executable
papers’ - embedded code or data

77. 3.4. Social Change! Some next steps:
• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne:
linking data to papers; develop virtual community around
that
• June 2011: ‘Executable Paper Challenge’ @ ICCS:
ask computer scientists to submit ideas for ‘executable
papers’ - embedded code or data
• August 2011: Dagstuhl Workshop ‘Future of Research
Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard):

78. 3.4. Social Change! Some next steps:
• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne:
linking data to papers; develop virtual community around
that
• June 2011: ‘Executable Paper Challenge’ @ ICCS:
ask computer scientists to submit ideas for ‘executable
papers’ - embedded code or data
• August 2011: Dagstuhl Workshop ‘Future of Research
Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard):
–Involve key parties (scientists, publishers, funding
bodies, libraries) to map out main bottlenecks

79. 3.4. Social Change! Some next steps:
• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne:
linking data to papers; develop virtual community around
that
• June 2011: ‘Executable Paper Challenge’ @ ICCS:
ask computer scientists to submit ideas for ‘executable
papers’ - embedded code or data
• August 2011: Dagstuhl Workshop ‘Future of Research
Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard):
–Involve key parties (scientists, publishers, funding
bodies, libraries) to map out main bottlenecks
–Write white paper

80. 3.4. Social Change! Some next steps:
• January 2011: ‘Beyond the PDF’ workshop, Phil Bourne:
linking data to papers; develop virtual community around
that
• June 2011: ‘Executable Paper Challenge’ @ ICCS:
ask computer scientists to submit ideas for ‘executable
papers’ - embedded code or data
• August 2011: Dagstuhl Workshop ‘Future of Research
Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard):
–Involve key parties (scientists, publishers, funding
bodies, libraries) to map out main bottlenecks
–Write white paper
–Implement?!

81. Questions? Interested in collaboration?
a.dewaard@elsevier.com
http://elsatglabs.com/labs/anita
15