The Story of Science:
   A plea for a syntagmatic/paradigmatic
   analysis of scientific text




   Anita de Waard, a.dewa...
Scientific papers are stories, that persuade
        with data




                             2


Thursday, October 21, 2...
Scientific papers are stories, that persuade
        with data
        1.Paradigmatic approach (Tropp)/
          story gra...
Scientific papers are stories, that persuade
        with data
        1.Paradigmatic approach (Tropp)/
          story gra...
Paradigmatic Approach: story grammar
The Story of Goldilocks              Story        Grammar     Paper              The ...
Paradigmatic Approach: story grammar
The Story of Goldilocks              Story        Grammar     Paper              The ...
Story structure also has a rhetorical goal:




                             4


Thursday, October 21, 2010
Story structure also has a rhetorical goal:
    Aristotle Quintilian                                                      ...
Story structure also has a rhetorical goal:
    Aristotle Quintilian                                                      ...
Paradigmatic approach for science



      Both seminomas and the EC component of
      nonseminomas share features with E...
Paradigmatic approach for science



      Both seminomas and the EC component of
       Both seminomas and the EC compone...
Paradigmatic approach for science



      Both seminomas and the EC component of
       Both seminomas and the EC compone...
Paradigmatic approach for science



      Both seminomas and the EC component of
       Both seminomas and the EC compone...
Paradigmatic approach for science



      Both seminomas and the EC component of
       Both seminomas and the EC compone...
Paradigmatic approach for science



      Both seminomas and the EC component of
       Both seminomas and the EC compone...
Paradigmatic approach for science



      Both seminomas and the EC component of
       Both seminomas and the EC compone...
Paradigmatic approach for science



      Both seminomas and the EC component of
       Both seminomas and the EC compone...
Paradigmatic approach for science



      Both seminomas and the EC component of
       Both seminomas and the EC compone...
Paradigmatic approach for science


                                                                           Conceptual
...
Paradigmatic approach for science


                                                                           Conceptual
...
Basic Segment Types




                             6


Thursday, October 21, 2010
Basic Segment Types
  Segment                    Description                         Example
  Fact                       ...
Paradigmatic analysis of clauses
 Conceptual discourse                       Connecting discourse       Experimental disco...
Realms in experimental discourse




Thursday, October 21, 2010
Realms in experimental discourse



     (1) Both seminomas        (2) b. the detection of
     and the EC component      ...
Realms in experimental discourse



     (1) Both seminomas                 (2) b. the detection of
     and the EC compon...
Realms in experimental discourse



     (1) Both seminomas                        (2) b. the detection of
     and the EC...
Realms in experimental discourse



     (1) Both seminomas                        (2) b. the detection of
     and the EC...
Realms in experimental discourse



     (1) Both seminomas                        (2) b. the detection of                ...
Realms in experimental discourse

                                              Concepts, models, ‘facts’

     (1) Both s...
Realms in experimental discourse

                                              Concepts, models, ‘facts’

     (1) Both s...
Realms in experimental discourse

                                              Concepts, models, ‘facts’

     (1) Both s...
Paradigmatic vs syntagmatic axes: use both?
 Paradigmatic                                                                 ...
Paradigmatic vs syntagmatic axes: use both?
 Paradigmatic                                                                 ...
Paradigmatic vs syntagmatic axes: use both?
 Paradigmatic                                                                 ...
Three dimensions of (semantic)annotation




                             measure




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




                             measure




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

        document
                   claim

     ...
Three dimensions of (semantic)annotation
Granularity
         collection

        document
                   claim

     ...
Three dimensions of (semantic)annotation
Granularity
         collection

        document
                   claim

     ...
Three dimensions of (semantic)annotation
Granularity
         collection

        document
                   claim

     ...
Three dimensions of (semantic)annotation
Granularity
         collection

        document
                   claim

     ...
Three dimensions of (semantic)annotation
Granularity
         collection

        document
                   claim

     ...
Syntagmatic analysis:
W3C HCLS ‘Ontology of Rhetorical Blocks’ (ORB)




                             11


Thursday, Octob...
Syntagmatic analysis:
W3C HCLS ‘Ontology of Rhetorical Blocks’ (ORB)




                             11


Thursday, Octob...
Syntagmatic enabler: Linked Data (for Elsevier)




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




      <ce:section id=#123>




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




                             this says
      <ce:section id=#123>     ...
Syntagmatic enabler: Linked Data (for Elsevier)




                                             said @anita
             ...
Syntagmatic enabler: Linked Data (for Elsevier)

                                                 but we all know
        ...
Syntagmatic enabler: Linked Data (for Elsevier)
      the xml is fixed, but the structure is open!
                       ...
Syntagmatic enabler: Linked Data (for Elsevier)
      the xml is fixed, but the structure is open!    allows for layers of...
Paradigmatic analysis: find segments using Verb form?




       1. An escape from oncogene-induced senescence is a prereq...
Paradigmatic analysis: find segments using Verb form?
  Manual analysis suggests a correlation:
  – Present: Fact (82%), H...
Paradigmatic analysis: find segments using Verb form?
  Manual analysis suggests a correlation:
  – Present: Fact (82%), H...
Paradigmatic analysis: find segments using Verb form?
  Manual analysis suggests a correlation:
  – Present: Fact (82%), H...
Paradigmatic analysis: find segments using Verb form?
  Manual analysis suggests a correlation:
  – Present: Fact (82%), H...
Paradigmatic analysis: find segments using Verb form?
  Manual analysis suggests a correlation:
  – Present: Fact (82%), H...
Summary Fact/Result/Hypothesis classification




                             14


Thursday, October 21, 2010
Summary Fact/Result/Hypothesis classification




                                  present -> Fact (64-44-76%)




       ...
Summary Fact/Result/Hypothesis classification




                                  present -> Fact (64-44-76%)
           ...
Summary Fact/Result/Hypothesis classification




                                  present -> Fact (64-44-76%)
           ...
Facts in the                Endogenous small RNAs (miRNAs) regulate I sing of golden-throned Hera whom Rhea
 eternal      ...
Biological Discourse Realms:
                             Topic, Discourse Progression, Truth

                           ...
Mythological Realms:Yggdrasil




Thursday, October 21, 2010
Questions?




                             18


Thursday, October 21, 2010
Questions?

          • Can we use these two types of classification - are
            they even different?
          • Wh...
Questions?




                             18


Thursday, October 21, 2010
Questions?




                                     a.dewaard@elsevier.com
                                  http://elsatg...
A syntagmatic and paradigmatic analysis of scientific text
A syntagmatic and paradigmatic analysis of scientific text
A syntagmatic and paradigmatic analysis of scientific text
A syntagmatic and paradigmatic analysis of scientific text
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Talk at the Workshop for Automated Motif Discovery in Cultural Heritage and Scientific Communication Texts, Vienna, October 21 2010

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A syntagmatic and paradigmatic analysis of scientific text

  1. 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. 2. Scientific papers are stories, that persuade with data 2 Thursday, October 21, 2010
  3. 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. 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. 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. 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. 7. Story structure also has a rhetorical goal: 4 Thursday, October 21, 2010
  8. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 21. Basic Segment Types 6 Thursday, October 21, 2010
  22. 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. 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. 24. Realms in experimental discourse Thursday, October 21, 2010
  25. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 36. Three dimensions of (semantic)annotation measure Thursday, October 21, 2010
  37. 37. Three dimensions of (semantic)annotation measure Thursday, October 21, 2010
  38. 38. Three dimensions of (semantic)annotation Granularity collection document claim triple entity measure Thursday, October 21, 2010
  39. 39. Three dimensions of (semantic)annotation Granularity collection document claim triple entity measure Means manual semi-automated automated Thursday, October 21, 2010
  40. 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. 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. 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. 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. 44. Syntagmatic analysis: W3C HCLS ‘Ontology of Rhetorical Blocks’ (ORB) 11 Thursday, October 21, 2010
  45. 45. Syntagmatic analysis: W3C HCLS ‘Ontology of Rhetorical Blocks’ (ORB) 11 Thursday, October 21, 2010
  46. 46. Syntagmatic enabler: Linked Data (for Elsevier) Thursday, October 21, 2010
  47. 47. Syntagmatic enabler: Linked Data (for Elsevier) <ce:section id=#123> Thursday, October 21, 2010
  48. 48. Syntagmatic enabler: Linked Data (for Elsevier) this says <ce:section id=#123> mice like cheese Thursday, October 21, 2010
  49. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 59. Summary Fact/Result/Hypothesis classification 14 Thursday, October 21, 2010
  60. 60. Summary Fact/Result/Hypothesis classification present -> Fact (64-44-76%) 14 Thursday, October 21, 2010
  61. 61. Summary Fact/Result/Hypothesis classification present -> Fact (64-44-76%) past -> Result (49-44-76%) 14 Thursday, October 21, 2010
  62. 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. 63. 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. 64. Biological Discourse Realms: Topic, Discourse Progression, Truth Conceptual Realm Topic Axis Epistemic Axis Discourse Progression Axis Experimental Realm Thursday, October 21, 2010
  65. 65. Mythological Realms:Yggdrasil Thursday, October 21, 2010
  66. 66. Questions? 18 Thursday, October 21, 2010
  67. 67. 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
  68. 68. Questions? 18 Thursday, October 21, 2010
  69. 69. Questions? a.dewaard@elsevier.com http://elsatglabs.com/labs/anita 18 Thursday, October 21, 2010

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