A syntagmatic/Paradigmatic analysis of scientific text

Syntagmatic/paradigmatic analysis of scientific text

Anita de Waard, [email protected] Disruptive Technologies Director, Elsevier Labs

University of Utrecht, Institute of Linguistics

HCLS Scientific Discourse CallMarch 28 2011

Saturday, March 26, 2011

mailto:[email protected]


Scientific papers are stories, that persuade with data

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1.Syntagmatic approach (Tropp)/story grammar (Rumelhart, Thorndyke): ‘‘systematic assignment of constituent structure”• Sequential components• Order in text is key factor• Granularity: one or more paragraphs (?)

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1.Syntagmatic 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.Paradigmatic 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’

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Syntagmatic analysis of fairytales:

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According to Propp, main characters (or dramatis personae) that are occuring in a fairy tale may be the following:1. Hero: a character that seeks something;2. Villain: opposes or actively blocks the heroʼs quest;3. Donor: provides the hero with an object of magical properties;4. Dispatcher: sends the hero on his/her quest via a message;5. False Hero: disrupts the heroʼs success by making false claims;6. Helper: aids the hero;7. Princess: acts as the reward for the hero and the object of the villainʼs plots;8. Her Father: acts to reward the hero for his effort.



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Morphology of the Folktale, Propp:“list of all the elements of the fairytale”. The list contains 150 elements, distributed over six tables:1. Initial Situation2. Preparatory Section3. Complication4. Donors5. From the Entry of the Helper to the End of the First Move6. Beginning of the Second Move



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Morphology of the Folktale, Propp:“list of all the elements of the fairytale”. The list contains 150 elements, distributed over six tables:1. Initial Situation2. Preparatory Section3. Complication4. Donors5. From the Entry of the Helper to the End of the First Move6. Beginning of the Second Move

F. Peinado, P. Gervas, and B. Diaz-Agudo, ʻA description logic ontology for fairy tale generationʼ, in Proceedings of LREC. ELRA, (5 2004)


Syntagmatic analysis of science: story grammar

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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 Goldilocks Characters

Setting

Objects of study the 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 Researchgoal

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 1 Name 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 domainShe 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), Saturday, March 26, 2011

Syntagmatic analysis of science: story grammar

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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 Goldilocks Characters

Setting

Objects of study the 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 Researchgoal

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 1 Name 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 domainShe 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), Saturday, March 26, 2011

http://www.sciencedirect.com/science?_ob=ArticleURL&_aset=V-WA-A-W-V-MsSAYZW-UUA-U-AACAVYEDAD-AAVEUDUCAD-YEEEYVDDW-V-U&_rdoc=2&_fmt=full&_udi=B6WSN-4GYG5B3-K&_coverDate=08%252F26%252F2005&_cdi=7051&_orig=search&_st=13&_sort=d&view=c&_acct=C000000593&_version=1&_urlVersion=0&_userid=3222073&md5=1fc244e0e7cfb82d0d6fdb19a49a89f9

http://www.sciencedirect.com/science?_ob=ArticleURL&_aset=V-WA-A-W-V-MsSAYZW-UUA-U-AACAVYEDAD-AAVEUDUCAD-YEEEYVDDW-V-U&_rdoc=2&_fmt=full&_udi=B6WSN-4GYG5B3-K&_coverDate=08%252F26%252F2005&_cdi=7051&_orig=search&_st=13&_sort=d&view=c&_acct=C000000593&_version=1&_urlVersion=0&_userid=3222073&md5=1fc244e0e7cfb82d0d6fdb19a49a89f9

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Rhetorical analogue to scientific structure:


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Aristotle QuintilianQuintilian 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

prothesisStatement 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

epilogos peroratio Following the refutatio and concluding the classical oration, the peroratio conventionally employed appeals through pathos, and often included a summing up.

Discussion: summary, implications.



http://rhetoric.byu.edu/Canons/Arrangement/Exordium.htm


http://rhetoric.byu.edu/Canons/Arrangement/Narratio.htm


http://rhetoric.byu.edu/Canons/Arrangement/Confirmatio.htm


http://rhetoric.byu.edu/Canons/Arrangement/Refutatio.htm


http://rhetoric.byu.edu/Canons/Arrangement/Peroratio.htm


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Aristotle QuintilianQuintilian 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

prothesisStatement 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

epilogos peroratio Following the refutatio and concluding the classical oration, the peroratio conventionally employed appeals through pathos, and often included a summing up.

Discussion: summary, implications.













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Syntagmatic analysis of scientific text: ORB vs. Medium-grained structure


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Syntagmatic analysis of scientific text: ORB vs. Medium-grained structure


Syntagmatic enabler: Linked Data (for Elsevier)



<ce:section id=#123>



<ce:section id=#123> mice like cheesethis says




said @anita on March 28, 2011

mice like cheesethis says


but we all know she was wrong then










the xml is fixed, but the structure is open!



allows for layers of annotation





the xml is fixed, but the structure is open!



Paradigmatic analysis of fairytales: The Structural Study of Myth, Claude Lévi-Strauss The Jnl of American Folklore, 68(270) pp. 428-44, 1955, “the true constituent units of a myth are not the isolated relations but bundles of such relations and it is only as bundles that these relations can be put to use and combined so as to produce a meaning. Relations pertaining to the same bundle may appear diachronically at remote intervals, but when we have succeeded in grouping them together, we have reorganized our myth according to a time referent of a new nature corresponding to the prerequisite of the initial hypothesis, namely,a two-dimensional time referent which is simultaneously diachronical and synchronical and which accordingly integrates the characteristics of the langue on one hand, and those of the parole on the other.”

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8



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(narrative) TIME



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(narrative) TIME

(narrative) THEME


Paradigmatic approach for science

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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 m i R - 3 7 1 - 3 e x p r e s s i n g s e m i n o m a s a n d nonseminomas, miR-302a-d was undetectable (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.



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Both seminomas and the EC component of nonseminomas share features with ES cells.To exclude thatthe 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 thatmiR-371-3 expression is a selective event during tumorigenesis.



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Fact



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Fact

Hypothesis



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Fact

Hypothesis

Method



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Fact

Hypothesis

Method

Result



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Fact

Hypothesis

Method

Result

Implication



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Fact

Hypothesis

Method

Result

Implication

Goal



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Fact

Hypothesis

Method

Result

Implication

Goal

Reg-Implication



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Fact

Hypothesis

Method

Result

Implication

Goal

Reg-Implication

Conceptual knowledge



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Fact

Hypothesis

Method

Result

Implication

Goal

Reg-Implication

Conceptual knowledge

ExperimentalEvidence


Realms in experimental discourse:


(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





(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







(2) a. To exclude that (3) b. suggesting that



(3) c. miR-371-3 expression is a selective event during tumorigenesis.













Concepts, models, ‘facts’










Experiment










Experiment

Transitions(2) a. To exclude that (3) b. suggesting that



Paradigmatic analysis of clausesConceptual 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.

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Mechanisms for realm transitions

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Mechanisms for realm transitions• Verb form change:

• Goal transitions:

• Regulatory segments:

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Whereas all three cluster-expressing cell lines contained high wt-p53 levels,NTera2 has low wild-type p53 levels,and NCCIT lost one p53 allelewhile the second allele is mutated (Burger et al, 1998).

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Additionally, we made a corresponding microarray (miR-Array) containing all miR-Lib inserts,which allows the detection of miRNA effects on proliferation.To test the sensitivity of screens with miR-Lib and miR-Array,We transduced modified primary BJ fibroblasts expressing ecotropic receptor...

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Additionally, we made a corresponding microarray (miR-Array) containing all miR-Lib inserts,which allows the detection of miRNA effects on proliferation.To test the sensitivity of screens with miR-Lib and miR-Array,We transduced modified primary BJ fibroblasts expressing ecotropic receptor...

In accordance, we observed an approximately 4-fold increase in miR311 signal, indicating that our procedure is sensitive enough to detect mild growth differences (Fig 1E).

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Paradigmatic vs syntagmatic axes: use both?

!

!

Experimental Realm

Syntagmatic Axis

Paradigmatic axis

This issue was addressed….

! Infusion of the highly selective D3 antagonists…!

A similar increase of recognition was obtained upon injection …!



!

These data suggest that !

Conceptual Realm !


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!

!

Experimental Realm

Syntagmatic Axis

Paradigmatic axis






!


Conceptual Realm !


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Paradigmatic: •repeats itself many times•‘fractal dimension’:

•course-grained: Introduction, Results, Discussion•medium-grained: parallel with paradigmatic?•fine-grained: level of clauses.



!

!

Experimental Realm

Syntagmatic Axis

Paradigmatic axis






!


Conceptual Realm !


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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’


Questions:

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Questions:

•What structures are useful to identify:•“Biological events”?•Modality/epistemic evaluation? •How do we connect to text structure?•Apply post-hoc or let authors create? •What new tools can we build on top of this?

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Questions:

•What structures are useful to identify:•“Biological events”?•Modality/epistemic evaluation? •How do we connect to text structure?•Apply post-hoc or let authors create? •What new tools can we build on top of this?

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[email protected]://elsatglabs.com/labs/anita




http://elsatglabs.com/labs/anita

http://elsatglabs.com/labs/anita

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A syntagmatic/Paradigmatic analysis of scientific text