A syntagmatic and paradigmatic analysis of scientific text

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, [email protected]
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
3
The Story of Goldilocks
and the Three Bears
Story Grammar Paper The AXH Domain of Ataxin-1 Mediates
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 GoldilocksCharacters
Setting
Objects of studythe Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
She went for a walk in the
forest. Pretty soon, she came
upon a house.
Location
Setting
Experimental
setup
studied and compared in vivo effects and interactions to those of
the human protein
She knocked and, when no one
answered,
Goal Theme Research
goal
Gain insight into how Atx-1's function contributes to SCA1
pathogenesis. How these interactions might contribute to the
disease process and how they might cause toxicity in only a subset
of neurons in SCA1 is not fully understood.
she walked right in. Attempt
Theme
Hypothesis Atx-1 may play a role in the regulation of gene expression
At the table in the kitchen, there
were three bowls of porridge.
Name Episode 1Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When
Overexpressed in Files
Goldilocks was hungry. Subgoal
Episode 1
Subgoal test the function of the AXH domain
She tasted the porridge from
the first bowl.
Attempt
Episode 1
Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand
and Perrimon, 1993) and compared its effects to those of hAtx-1.
This porridge is too hot! she
exclaimed.
Outcome
Episode 1
Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives
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
Atx-1 does not show obvious morphological changes in the
photoreceptor cells
So, she tasted the porridge
from the second bowl.
Activity
Episode 1
Data (data not shown),
This porridge is too cold, she
said
Outcome
Episode 1
Results both genotypes show many large holes and loss of cell integrity at
28 days
So, she tasted the last bowl of
porridge.
 Activity
Episode 1
Data (Figures 1B-1D).
Ahhh, this porridge is just right,
she said happily and
Outcome
Episode 1
Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces
eye abnormalities. The external structures of the eyes that
overexpress dAtx-1 show disorganized ommatidia and loss of
interommatidial bristles
she ate it all up.  
Episode 1
Data (Figure 1F),
Thursday, October 21, 2010

6. Paradigmatic Approach: story grammar
3
The Story of Goldilocks
and the Three Bears
Story Grammar Paper The AXH Domain of Ataxin-1 Mediates
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 GoldilocksCharacters
Setting
Objects of studythe Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
She went for a walk in the
forest. Pretty soon, she came
upon a house.
Location
Setting
Experimental
setup
studied and compared in vivo effects and interactions to those of
the human protein
She knocked and, when no one
answered,
Goal Theme Research
goal
Gain insight into how Atx-1's function contributes to SCA1
pathogenesis. How these interactions might contribute to the
disease process and how they might cause toxicity in only a subset
of neurons in SCA1 is not fully understood.
she walked right in. Attempt
Theme
Hypothesis Atx-1 may play a role in the regulation of gene expression
At the table in the kitchen, there
were three bowls of porridge.
Name Episode 1Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When
Overexpressed in Files
Goldilocks was hungry. Subgoal
Episode 1
Subgoal test the function of the AXH domain
She tasted the porridge from
the first bowl.
Attempt
Episode 1
Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand
and Perrimon, 1993) and compared its effects to those of hAtx-1.
This porridge is too hot! she
exclaimed.
Outcome
Episode 1
Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives
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
Atx-1 does not show obvious morphological changes in the
photoreceptor cells
So, she tasted the porridge
from the second bowl.
Activity
Episode 1
Data (data not shown),
This porridge is too cold, she
said
Outcome
Episode 1
Results both genotypes show many large holes and loss of cell integrity at
28 days
So, she tasted the last bowl of
porridge.
 Activity
Episode 1
Data (Figures 1B-1D).
Ahhh, this porridge is just right,
she said happily and
Outcome
Episode 1
Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces
eye abnormalities. The external structures of the eyes that
overexpress dAtx-1 show disorganized ommatidia and loss of
interommatidial bristles
she ate it all up.  
Episode 1
Data (Figure 1F),
Thursday, October 21, 2010

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

8. 4
AristotleQuintilianQuintilian Scientific Paper
prooimion
Introduction
/ exordium
The introduction of a speech, where one announces the
subject and purpose of the discourse, and where one usually
employs the persuasive appeal to ethos in order to
establish credibility with the audience.
Introduction:
positioning
prothesis
Statement of
Facts/narratio
The speaker here provides a narrative account of what has
happened and generally explains the nature of the case.
Introduction: research
question
 
Summary/
propostitio
The propositio provides a brief summary of what one is about
to speak on, or concisely puts forth the charges or accusation.
Summary of contents
pistis
Proof/
confirmatio
The main body of the speech where one offers logical
arguments as proof. The appeal to logos is emphasized
here.
Results
 
Refutation/
refutatio
As the name connotes, this section of a speech was devoted to
answering the counterarguments of one's opponent.
Related Work
epilogosperoratio 
Following the refutatio and concluding the classical oration, the
peroratio conventionally employed appeals through
pathos, and often included a summing up.
Discussion: summary,
implications.
Story structure also has a rhetorical goal:
Thursday, October 21, 2010

9. 4
AristotleQuintilianQuintilian Scientific Paper
prooimion
Introduction
/ exordium
The introduction of a speech, where one announces the
subject and purpose of the discourse, and where one usually
employs the persuasive appeal to ethos in order to
establish credibility with the audience.
Introduction:
positioning
prothesis
Statement of
Facts/narratio
The speaker here provides a narrative account of what has
happened and generally explains the nature of the case.
Introduction: research
question
 
Summary/
propostitio
The propositio provides a brief summary of what one is about
to speak on, or concisely puts forth the charges or accusation.
Summary of contents
pistis
Proof/
confirmatio
The main body of the speech where one offers logical
arguments as proof. The appeal to logos is emphasized
here.
Results
 
Refutation/
refutatio
As the name connotes, this section of a speech was devoted to
answering the counterarguments of one's opponent.
Related Work
epilogosperoratio 
Following the refutatio and concluding the classical oration, the
peroratio conventionally employed appeals through
pathos, and often included a summing up.
Discussion: summary,
implications.
Story structure also has a rhetorical goal:
Thursday, October 21, 2010

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

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

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

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

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

15. Paradigmatic approach for science
5
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.
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.
Fact
Hypothesis
Method
Result
Thursday, October 21, 2010

16. Paradigmatic approach for science
5
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.
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.
Fact
Hypothesis
Method
Result
Implication
Thursday, October 21, 2010

17. Paradigmatic approach for science
5
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.
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.
Fact
Hypothesis
Method
Result
Implication
Goal
Thursday, October 21, 2010

18. Paradigmatic approach for science
5
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.
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.
Fact
Hypothesis
Method
Result
Implication
Goal
Reg-Implication
Thursday, October 21, 2010

19. Paradigmatic approach for science
5
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.
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.
Fact
Hypothesis
Method
Result
Implication
Goal
Reg-Implication
Conceptual
knowledge
Thursday, October 21, 2010

20. Paradigmatic approach for science
5
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.
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.
Fact
Hypothesis
Method
Result
Implication
Goal
Reg-Implication
Conceptual
knowledge
Experimental
Evidence
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
without explicit citation
mature miR-373 is a homolog of miR-372
Hypothesis a proposed idea, not supported
by evidence
This could for instance be a result of high
mdm2 levels
Problem unresolved, contradictory, or
unclear issue
However, further investigation is required to
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
an experiment
all constructs yielded high expression levels
of mature miRNAs
Implication an interpretation of the results,
in light of earlier hypotheses
and facts
our procedure is sensitive enough to detect
mild growth differences
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. (1) Both seminomas
and the EC component
of nonseminomas share
features with ES cells.
(2) b. the detection of
miR-371-3 merely
reflects its expression
pattern in ES cells,
Realms in experimental discourse
Thursday, October 21, 2010

26. (1) Both seminomas
and the EC component
of nonseminomas share
features with ES cells.
(2) b. the detection of
miR-371-3 merely
reflects its expression
pattern in ES cells,
(2) a. To exclude that
Realms in experimental discourse
Thursday, October 21, 2010

27. (1) Both seminomas
and the EC component
of nonseminomas share
features with ES cells.
(2) b. the detection of
miR-371-3 merely
reflects its expression
pattern in ES cells,
(2) c. we tested by RPA
miR-302a-d, another ES
cells-specific miRNA cluster
(Suh et al, 2004).
(3) a. In many of the miR-371-3
expressing seminomas and
nonseminomas, miR-302a-d was
undetectable (Figs S7 and S8),
(2) a. To exclude that
Realms in experimental discourse
Thursday, October 21, 2010

28. (1) Both seminomas
and the EC component
of nonseminomas share
features with ES cells.
(2) b. the detection of
miR-371-3 merely
reflects its expression
pattern in ES cells,
(2) c. we tested by RPA
miR-302a-d, another ES
cells-specific miRNA cluster
(Suh et al, 2004).
(3) a. In many of the miR-371-3
expressing seminomas and
nonseminomas, miR-302a-d was
undetectable (Figs S7 and S8),
(2) a. To exclude that (3) b. suggesting that
Realms in experimental discourse
Thursday, October 21, 2010

29. (3) c. miR-371-3
expression is a
selective event during
tumorigenesis.
(1) Both seminomas
and the EC component
of nonseminomas share
features with ES cells.
(2) b. the detection of
miR-371-3 merely
reflects its expression
pattern in ES cells,
(2) c. we tested by RPA
miR-302a-d, another ES
cells-specific miRNA cluster
(Suh et al, 2004).
(3) a. In many of the miR-371-3
expressing seminomas and
nonseminomas, miR-302a-d was
undetectable (Figs S7 and S8),
(2) a. To exclude that (3) b. suggesting that
Realms in experimental discourse
Thursday, October 21, 2010

30. (3) c. miR-371-3
expression is a
selective event during
tumorigenesis.
(1) Both seminomas
and the EC component
of nonseminomas share
features with ES cells.
(2) b. the detection of
miR-371-3 merely
reflects its expression
pattern in ES cells,
(2) c. we tested by RPA
miR-302a-d, another ES
cells-specific miRNA cluster
(Suh et al, 2004).
(3) a. In many of the miR-371-3
expressing seminomas and
nonseminomas, miR-302a-d was
undetectable (Figs S7 and S8),
Concepts, models, ‘facts’
(2) a. To exclude that (3) b. suggesting that
Realms in experimental discourse
Thursday, October 21, 2010

31. (3) c. miR-371-3
expression is a
selective event during
tumorigenesis.
(1) Both seminomas
and the EC component
of nonseminomas share
features with ES cells.
(2) b. the detection of
miR-371-3 merely
reflects its expression
pattern in ES cells,
(2) c. we tested by RPA
miR-302a-d, another ES
cells-specific miRNA cluster
(Suh et al, 2004).
(3) a. In many of the miR-371-3
expressing seminomas and
nonseminomas, miR-302a-d was
undetectable (Figs S7 and S8),
Concepts, models, ‘facts’
Experiment
(2) a. To exclude that (3) b. suggesting that
Realms in experimental discourse
Thursday, October 21, 2010

32. (3) c. miR-371-3
expression is a
selective event during
tumorigenesis.
(1) Both seminomas
and the EC component
of nonseminomas share
features with ES cells.
(2) b. the detection of
miR-371-3 merely
reflects its expression
pattern in ES cells,
(2) c. we tested by RPA
miR-302a-d, another ES
cells-specific miRNA cluster
(Suh et al, 2004).
(3) a. In many of the miR-371-3
expressing seminomas and
nonseminomas, miR-302a-d was
undetectable (Figs S7 and S8),
Concepts, models, ‘facts’
Experiment
Transitions(2) a. To exclude that (3) b. suggesting that
Realms in experimental discourse
Thursday, October 21, 2010

33. Paradigmatic vs syntagmatic axes: use both?
!
!
Experimental Rea lm
Syntagmatic Axis

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

34. Paradigmatic vs syntagmatic axes: use both?
!
!
Experimental Rea lm
Syntagmatic Axis

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

35. Paradigmatic vs syntagmatic axes: use both?
!
!
Experimental Rea lm
Syntagmatic Axis

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

triple

entity
collection
Granularity
Three dimensions of (semantic)annotation
measure
Thursday, October 21, 2010

39. document
claim

triple

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

40. document
claim

triple

entity
collection
Granularity
Three dimensions of (semantic)annotation
reader/curator/data miningtypesetter/productionauthor/editor
Moment
automated
manual
semi-automated
Means
measure
Thursday, October 21, 2010

41. document
claim

triple

entity
collection
Granularity
Three dimensions of (semantic)annotation
Web-Based Protein Markup
reader/curator/data miningtypesetter/productionauthor/editor
Moment
automated
manual
semi-automated
Means
measure
Thursday, October 21, 2010

42. document
claim

triple

entity
collection
Granularity
Three dimensions of (semantic)annotation
Hypothesis markup
Web-Based Protein Markup
reader/curator/data miningtypesetter/productionauthor/editor
Moment
automated
manual
semi-automated
Means
measure
Thursday, October 21, 2010

43. document
claim

triple

entity
collection
Granularity
Three dimensions of (semantic)annotation
Hypothesis markup
Web-Based Protein Markup
reader/curator/data miningtypesetter/productionauthor/editor
Moment
automated
manual
semi-automated
Means
measure
Thursday, October 21, 2010

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

45. 11
Syntagmatic analysis:
W3C HCLS ‘Ontology of Rhetorical Blocks’ (ORB)
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)
<ce:section id=#123> mice like cheese
this says
Thursday, October 21, 2010

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

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

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

52. allows for layers of annotation
but we all know
she was wrong then
Syntagmatic enabler: Linked Data (for Elsevier)
<ce:section id=#123>
said @anita
on September 8, 2010
the xml is fixed, but the structure is open!
mice like cheese
this says
Thursday, October 21, 2010

53. Paradigmatic analysis: find segments using Verb form?
131.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
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%)
131.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
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:
131.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
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?
131.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
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:
131.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
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:
131.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
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. Facts in the
eternal
present
Endogenous small RNAs (miRNAs) regulate
gene expression by mechanisms conserved
across metazoans.
I sing of golden-throned Hera whom Rhea
bare. Queen of the immortals is she, surpassing
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
simple past
Vehicle-treated animals spent equivalent
time investigating a juvenile in the first and
second sessions in experiments
conducted in the NAC and the striatum:
T1 values were 122 ± 6 s and 114 ± 5 s.
Now the wooers turned to the dance and to
gladsome song, and made them merry, and
waited till evening should come; and as they
made merry dark evening came upon them.
Events with
embedded
facts
We also generated BJ/ET cells expressing
the RASV12-ERTAM chimera gene, which is
only active when tamoxifen is added (De
Vita et al, 2005).
And she took her mighty spear, tipped with
sharp bronze, heavy and huge and strong,
wherewith she vanquishes the ranks of men-of
warriors, with whom she is wroth, she, the
daughter of the mighty sire.
Attribution
in the
present
perfect
miRNAs have emerged as important
regulators of development and control
processes such as cell fate determination
and cell death (Abrahante et al., 2003,
Brennecke et al., 2003, Chang et al., 2004,
Chen et al., 2004, Johnston and Hobert,
2003, Lee et al., 1993, ...
In this book I have had old stories written
down, as I have heard them told by intelligent
people, concerning chiefs who have held
dominion in the northern countries, and who
spoke the Danish tongue; and also concerning
some of their family branches, according to
what has been told me.
Implications
are hedged,
and in the
present
tense
These results indicate that although
miR-372&3 confer complete protection to
oncogene-induced senescence in a manner
similar to p53 inactivation, the cellular
response to DNA damage remains intact
Now it is said that ever since then
whenever the camel sees a place where ashes
have been scattered, he wants to get revenge
with his enemy the rat and stomps and rolls in
the ashes hoping to get the rat
Parallels in tense use between science and mythology
Thursday, October 21, 2010

64. Biological Discourse Realms relevant to tense use:
Topic (syntagmatic), Discourse Progression
(paradigmatic), Truth (trust)

Conceptual Realm
Experimental Realm
Discourse Progression
Axis

Epistemic Axis
Topic Axis
16
Thursday, October 21, 2010

65. Biological Discourse Realms relevant to tense use:
Topic (syntagmatic), Discourse Progression
(paradigmatic), Truth (trust)

Conceptual Realm
Experimental Realm
Discourse Progression
Axis

Epistemic Axis
Topic Axis
16
Present
Thursday, October 21, 2010

66. Biological Discourse Realms relevant to tense use:
Topic (syntagmatic), Discourse Progression
(paradigmatic), Truth (trust)

Conceptual Realm
Experimental Realm
Discourse Progression
Axis

Epistemic Axis
Topic Axis
16
Present
Past
Thursday, October 21, 2010

67. Biological Discourse Realms relevant to tense use:
Topic (syntagmatic), Discourse Progression
(paradigmatic), Truth (trust)

Conceptual Realm
Experimental Realm
Discourse Progression
Axis

Epistemic Axis
Topic Axis
16
Present
Past
Past, Present
Thursday, October 21, 2010

68. Biological Discourse Realms relevant to tense use:
Topic (syntagmatic), Discourse Progression
(paradigmatic), Truth (trust)

Conceptual Realm
Experimental Realm
Discourse Progression
Axis

Epistemic Axis
Topic Axis
16
Past Perfect
Present
Past
Past, Present
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?
18
[email protected]
http://elsatglabs.com/labs/anita
Thursday, October 21, 2010