Talk at the Workshop for Automated Motif Discovery in Cultural Heritage and Scientific Communication Texts, Vienna, October 21 2010

1. The Story of Science:
A plea for a syntagmatic/paradigmatic
analysis of scientific text
Anita de Waard, a.dewaard@elsevier.com
Disruptive Technologies Director, Elsevier Labs
University of Utrecht, Institute of Linguistics
Thursday, October 21, 2010

2. Scientific papers are stories, that persuade
with data
2
Thursday, October 21, 2010

3. Scientific papers are stories, that persuade
with data
1.Paradigmatic approach (Tropp)/
story grammar (Rumelhart, Thorndyke):
‘‘systematic assignment of constituent structure”
• Sequential components
• Order in text is key factor
• Granularity: one or more paragraphs (?)
2
Thursday, October 21, 2010

4. Scientific papers are stories, that persuade
with data
1.Paradigmatic approach (Tropp)/
story grammar (Rumelhart, Thorndyke):
‘‘systematic assignment of constituent structure”
• Sequential components
• Order in text is key factor
• Granularity: one or more paragraphs (?)
2.Syntagmatic approach:
“groups of relations between actors and events are
sought throughout the text” (Lévi-Strauss, 1955)
• Groups are found throughout the text
• Relationship types between actors/events are key
• Granularity: ‘shortest possible sentences’
2
Thursday, October 21, 2010

5. Paradigmatic Approach: story grammar
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
3 overexpress dAtx-1 show disorganized ommatidia and loss of
she ate it all up. Data interommatidial bristles
(Figure 1F),
Thursday, October 21, 2010

6. Paradigmatic Approach: story grammar
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
3 overexpress dAtx-1 show disorganized ommatidia and loss of
she ate it all up. Data interommatidial bristles
(Figure 1F),
Thursday, October 21, 2010

7. Story structure also has a rhetorical goal:
4
Thursday, October 21, 2010

8. Story structure also has a rhetorical goal:
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
pathos, and often included a summing up. implications.
4
Thursday, October 21, 2010

9. Story structure also has a rhetorical goal:
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
pathos, and often included a summing up. implications.
4
Thursday, October 21, 2010

10. Paradigmatic approach for science
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.
5
Thursday, October 21, 2010

11. Paradigmatic approach for science
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.
5
Thursday, October 21, 2010

12. Paradigmatic approach for science
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.
5
Thursday, October 21, 2010

13. Paradigmatic approach for science
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.
5
Thursday, October 21, 2010

14. Paradigmatic approach for science
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.
5
Thursday, October 21, 2010

15. Paradigmatic approach for science
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.
5
Thursday, October 21, 2010

16. Paradigmatic approach for science
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.
5
Thursday, October 21, 2010

17. Paradigmatic approach for science
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.
5
Thursday, October 21, 2010

18. Paradigmatic approach for science
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.
5
Thursday, October 21, 2010

19. Paradigmatic approach for science
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.
5
Thursday, October 21, 2010

20. Paradigmatic approach for science
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.
5
Thursday, October 21, 2010

21. Basic Segment Types
6
Thursday, October 21, 2010

22. Basic Segment Types
Segment Description Example
Fact a known fact, generally mature miR-373 is a homolog of miR-372
without explicit citation
Hypothesis a proposed idea, not supported This could for instance be a result of high
by evidence mdm2 levels
Problem unresolved, contradictory, or However, further investigation is required to
unclear issue demonstrate the exact mechanism of LATS2
action
Goal research goal To identify novel functions of miRNAs,
Method experimental method Using fluorescence microscopy and luciferase
assays,
Result a restatement of the outcome of all constructs yielded high expression levels
an experiment of mature miRNAs
Implication an interpretation of the results, our procedure is sensitive enough to detect
in light of earlier hypotheses mild growth differences
and facts
6
Thursday, October 21, 2010

23. Paradigmatic analysis of clauses
Conceptual discourse Connecting discourse Experimental discourse
Though D3 receptor antagonists can
enhance cognitive function,
their sites of action remain unexplored.
This issue was addressed
employing a model of social recognition in rats,
and the actions of D3 antagonists were compared to
D1 agonists
that likewise possess pro-cognitive
properties.
Infusion of the highly selective D3 antagonists,
S33084 and SB277,011 (0.04-2.5 µg/side), into the
frontal cortex (FCX) dose-dependently reversed the
deficit in recognition induced by a delay.
By contrast, the preferential D2 antagonist, L741,626
(0.63-5.0) had no effect.
The action of S33084 was regionally specific
inasmuch as its injection into the nucleus accumbens
or striatum was ineffective.
These data suggest that
D3 receptors modulating social
recognition are localized in FCX,
and underpin their pertinence as targets
for antipsychotic agents.
Thursday, October 21, 2010

24. Realms in experimental discourse
Thursday, October 21, 2010

25. 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,
Thursday, October 21, 2010

26. 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
Thursday, October 21, 2010

27. 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),
Thursday, October 21, 2010

28. 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),
Thursday, October 21, 2010

29. 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),
Thursday, October 21, 2010

30. 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),
Thursday, October 21, 2010

31. 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
Thursday, October 21, 2010

32. 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
Thursday, October 21, 2010

33. Paradigmatic vs syntagmatic axes: use both?
Paradigmatic Conceptual Realm
axis Though D3 receptor antagonists ! !
can enhance cognitive function,
D3 receptors modulating social
recognition are localized in FCX,
their sites of action remain
unexplored. !
This issue was These data suggest that
addressed…. ! Syntagmatic Axis
! Infusion of the highly
selective D3 antagonists…!
A similar increase of recognition
was obtained upon injection …!
Experimental Realm
9
Thursday, October 21, 2010

34. Paradigmatic vs syntagmatic axes: use both?
Paradigmatic Conceptual Realm
axis Though D3 receptor antagonists ! !
can enhance cognitive function,
D3 receptors modulating social
recognition are localized in FCX,
their sites of action remain
unexplored. !
This issue was These data suggest that
addressed…. ! Syntagmatic Axis
! Infusion of the highly
selective D3 antagonists…!
A similar increase of recognition
was obtained upon injection …!
Experimental Realm
Paradigmatic:
•repeats itself many times
•‘fractal dimension’:
•course-grained: Introduction, Results, Discussion
•medium-grained: parallel with paradigmatic?
•fine-grained: level of clauses.
9
Thursday, October 21, 2010

35. Paradigmatic vs syntagmatic axes: use both?
Paradigmatic Conceptual Realm
axis Though D3 receptor antagonists ! !
can enhance cognitive function,
D3 receptors modulating social
recognition are localized in FCX,
their sites of action remain
unexplored. !
This issue was These data suggest that
addressed…. ! Syntagmatic Axis
! Infusion of the highly
selective D3 antagonists…!
A similar increase of recognition
was obtained upon injection …!
Experimental Realm
Paradigmatic: Syntagmatic:
•repeats itself many times • single line?
•‘fractal dimension’: • order is essential
•course-grained: Introduction, Results, Discussion •‘medium-grained - ‘story components’
•medium-grained: parallel with paradigmatic?
•fine-grained: level of clauses.
9
Thursday, October 21, 2010

36. Three dimensions of (semantic)annotation
measure
Thursday, October 21, 2010

37. Three dimensions of (semantic)annotation
measure
Thursday, October 21, 2010

38. Three dimensions of (semantic)annotation
Granularity
collection
document
claim
triple
entity
measure
Thursday, October 21, 2010

39. Three dimensions of (semantic)annotation
Granularity
collection
document
claim
triple
entity
measure
Means manual
semi-automated
automated
Thursday, October 21, 2010

40. Three dimensions of (semantic)annotation
Granularity
collection
document
claim
triple
entity Mome
measure author/editor typesetter/production reader/curator/data m
Means manual
semi-automated
automated
Thursday, October 21, 2010

41. Three dimensions of (semantic)annotation
Granularity
collection
document
claim
triple
entity Mome
measure author/editor typesetter/production reader/curator/data m
Means manual
semi-automated Web-Based Protein Markup
automated
Thursday, October 21, 2010

42. Three dimensions of (semantic)annotation
Granularity
collection
document
claim
triple Hypothesis markup
entity Mome
measure author/editor typesetter/production reader/curator/data m
Means manual
semi-automated Web-Based Protein Markup
automated
Thursday, October 21, 2010

43. Three dimensions of (semantic)annotation
Granularity
collection
document
claim
triple Hypothesis markup
entity Mome
measure author/editor typesetter/production reader/curator/data m
Means manual
semi-automated Web-Based Protein Markup
automated
Thursday, October 21, 2010

44. Syntagmatic analysis:
W3C HCLS ‘Ontology of Rhetorical Blocks’ (ORB)
11
Thursday, October 21, 2010

45. Syntagmatic analysis:
W3C HCLS ‘Ontology of Rhetorical Blocks’ (ORB)
11
Thursday, October 21, 2010

46. Syntagmatic enabler: Linked Data (for Elsevier)
Thursday, October 21, 2010

47. Syntagmatic enabler: Linked Data (for Elsevier)
<ce:section id=#123>
Thursday, October 21, 2010

48. Syntagmatic enabler: Linked Data (for Elsevier)
this says
<ce:section id=#123> mice like cheese
Thursday, October 21, 2010

49. Syntagmatic enabler: Linked Data (for Elsevier)
said @anita
on September 8, 2010
this says
<ce:section id=#123> mice like cheese
Thursday, October 21, 2010

50. Syntagmatic enabler: Linked Data (for Elsevier)
but we all know
she was wrong then
said @anita
on September 8, 2010
this says
<ce:section id=#123> mice like cheese
Thursday, October 21, 2010

51. Syntagmatic enabler: Linked Data (for Elsevier)
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
Thursday, October 21, 2010

52. Syntagmatic enabler: Linked Data (for Elsevier)
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
Thursday, October 21, 2010

53. Paradigmatic analysis: find segments using Verb form?
1. An escape from oncogene-induced senescence is a prerequisite for full
transformation into tumor cells.
2. An escape from oncogene-induced senescence was a prerequisite for full
transformation into tumor cells.
3. An escape from oncogene-induced senescence may be a prerequisite for
full transformation into tumor cells
13
Thursday, October 21, 2010

54. Paradigmatic analysis: find segments using Verb form?
Manual analysis suggests a correlation:
– Present: Fact (82%), Hypothesis (71%), Implication (62%)
– Past: Result (82%), Method (76%) - 50% Passive, of
Method 50% Past Perfect
– Modal: Hypothesis (44%)
1. An escape from oncogene-induced senescence is a prerequisite for full
transformation into tumor cells.
2. An escape from oncogene-induced senescence was a prerequisite for full
transformation into tumor cells.
3. An escape from oncogene-induced senescence may be a prerequisite for
full transformation into tumor cells
13
Thursday, October 21, 2010

55. Paradigmatic analysis: find segments using Verb form?
Manual analysis suggests a correlation:
– Present: Fact (82%), Hypothesis (71%), Implication (62%)
– Past: Result (82%), Method (76%) - 50% Passive, of
Method 50% Past Perfect
– Modal: Hypothesis (44%)
Experiment:
1. An escape from oncogene-induced senescence is a prerequisite for full
transformation into tumor cells.
2. An escape from oncogene-induced senescence was a prerequisite for full
transformation into tumor cells.
3. An escape from oncogene-induced senescence may be a prerequisite for
full transformation into tumor cells
13
Thursday, October 21, 2010

56. Paradigmatic analysis: find segments using Verb form?
Manual analysis suggests a correlation:
– Present: Fact (82%), Hypothesis (71%), Implication (62%)
– Past: Result (82%), Method (76%) - 50% Passive, of
Method 50% Past Perfect
– Modal: Hypothesis (44%)
Experiment:
–Does verb tense determine perceived segment type?
1. An escape from oncogene-induced senescence is a prerequisite for full
transformation into tumor cells.
2. An escape from oncogene-induced senescence was a prerequisite for full
transformation into tumor cells.
3. An escape from oncogene-induced senescence may be a prerequisite for
full transformation into tumor cells
13
Thursday, October 21, 2010

57. Paradigmatic analysis: find segments using Verb form?
Manual analysis suggests a correlation:
– Present: Fact (82%), Hypothesis (71%), Implication (62%)
– Past: Result (82%), Method (76%) - 50% Passive, of
Method 50% Past Perfect
– Modal: Hypothesis (44%)
Experiment:
–Does verb tense determine perceived segment type?
–Manual classification of 104 tense-manipulated segments:
1. An escape from oncogene-induced senescence is a prerequisite for full
transformation into tumor cells.
2. An escape from oncogene-induced senescence was a prerequisite for full
transformation into tumor cells.
3. An escape from oncogene-induced senescence may be a prerequisite for
full transformation into tumor cells
13
Thursday, October 21, 2010

58. Paradigmatic analysis: find segments using Verb form?
Manual analysis suggests a correlation:
– Present: Fact (82%), Hypothesis (71%), Implication (62%)
– Past: Result (82%), Method (76%) - 50% Passive, of
Method 50% Past Perfect
– Modal: Hypothesis (44%)
Experiment:
–Does verb tense determine perceived segment type?
–Manual classification of 104 tense-manipulated segments:
1. An escape from oncogene-induced senescence is a prerequisite for full
transformation into tumor cells.
2. An escape from oncogene-induced senescence was a prerequisite for full
transformation into tumor cells.
3. An escape from oncogene-induced senescence may be a prerequisite for
full transformation into tumor cells
13
Thursday, October 21, 2010

59. Summary Fact/Result/Hypothesis classification
14
Thursday, October 21, 2010

60. Summary Fact/Result/Hypothesis classification
present -> Fact (64-44-76%)
14
Thursday, October 21, 2010

61. Summary Fact/Result/Hypothesis classification
present -> Fact (64-44-76%)
past -> Result (49-44-76%)
14
Thursday, October 21, 2010

62. Summary Fact/Result/Hypothesis classification
present -> Fact (64-44-76%)
past -> Result (49-44-76%)
modal -> Hypothesis (33-46-39%)
14
Thursday, October 21, 2010

63. Parallels in tense use between science and mythology
Facts in the Endogenous small RNAs (miRNAs) regulate I sing of golden-throned Hera whom Rhea
eternal gene expression by mechanisms conserved bare. Queen of the immortals is she, surpassing
present across metazoans. all in beauty: she is the sister and the wife of
loud-thundering Zeus, --the glorious one whom
all the blessed throughout high Olympus
reverence and honor.
Events in the Vehicle-treated animals spent equivalent Now the wooers turned to the dance and to
simple past time investigating a juvenile in the first and gladsome song, and made them merry, and
second sessions in experiments waited till evening should come; and as they
conducted in the NAC and the striatum: made merry dark evening came upon them.
T1 values were 122 ± 6 s and 114 ± 5 s.
Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped with
embedded the RASV12-ERTAM chimera gene, which is sharp bronze, heavy and huge and strong,
facts only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-of
Vita et al, 2005). warriors, with whom she is wroth, she, the
daughter of the mighty sire.
Attribution miRNAs have emerged as important In this book I have had old stories written
in the regulators of development and control down, as I have heard them told by intelligent
present processes such as cell fate determination people, concerning chiefs who have held
perfect and cell death (Abrahante et al., 2003, dominion in the northern countries, and who
Brennecke et al., 2003, Chang et al., 2004, spoke the Danish tongue; and also concerning
Chen et al., 2004, Johnston and Hobert, some of their family branches, according to
2003, Lee et al., 1993, ... what has been told me.
Implications These results indicate that although Now it is said that ever since then
are hedged, miR-372&3 confer complete protection to whenever the camel sees a place where ashes
and in the oncogene-induced senescence in a manner have been scattered, he wants to get revenge
present similar to p53 inactivation, the cellular with his enemy the rat and stomps and rolls in
tense response to DNA damage remains intact the ashes hoping to get the rat
Thursday, October 21, 2010

64. Biological Discourse Realms relevant to tense use:
Topic (syntagmatic), Discourse Progression
(paradigmatic), Truth (trust)
Conceptual Realm
Topic Axis
Epistemic Axis
Discourse Progression
Axis
Experimental Realm
16
Thursday, October 21, 2010

65. Biological Discourse Realms relevant to tense use:
Topic (syntagmatic), Discourse Progression
(paradigmatic), Truth (trust)
Conceptual Realm
Topic Axis
Present
Epistemic Axis
Discourse Progression
Axis
Experimental Realm
16
Thursday, October 21, 2010

66. Biological Discourse Realms relevant to tense use:
Topic (syntagmatic), Discourse Progression
(paradigmatic), Truth (trust)
Conceptual Realm
Topic Axis
Present
Epistemic Axis
Discourse Progression
Axis
Past
Experimental Realm
16
Thursday, October 21, 2010

67. Biological Discourse Realms relevant to tense use:
Topic (syntagmatic), Discourse Progression
(paradigmatic), Truth (trust)
Conceptual Realm
Topic Axis
Present
Past, Present
Epistemic Axis
Discourse Progression
Axis
Past
Experimental Realm
16
Thursday, October 21, 2010

68. Biological Discourse Realms relevant to tense use:
Topic (syntagmatic), Discourse Progression
(paradigmatic), Truth (trust)
Conceptual Realm
Topic Axis
Present
Past Perfect Past, Present
Epistemic Axis
Discourse Progression
Axis
Past
Experimental Realm
16
Thursday, October 21, 2010

69. Mythological Realms: Yggdrasil
17
Thursday, October 21, 2010

70. Questions?
18
Thursday, October 21, 2010

71. Questions?
• Can we use these two types of classification - are
they even different?
• What structure/ontology/classes?
• Valid for which texts?
• Apply post-hoc or let authors create?
• How do we use: for machine or user access?
18
Thursday, October 21, 2010

72. Questions?
18
Thursday, October 21, 2010

73. Questions?
a.dewaard@elsevier.com
http://elsatglabs.com/labs/anita
18
Thursday, October 21, 2010