‘These results suggest that...’                         Knowledge Attribution in                           Scientific Disco...
How a claim becomes a fact:   -       Voorhoeve, 2006: “These miRNAs neutralize p53- mediated CDK           inhibition, po...
“[Y]ou can transform a fact into fiction or a fiction into fact                      just by adding or subtracting reference...
“[Y]ou can transform a fact into fiction or a fiction into fact                      just by adding or subtracting reference...
Research Questions:Monday, April 2, 2012
Research Questions:       1. Can we find a model for epistemic evaluation and knowledge          attribution to describe al...
Research Questions:       1. Can we find a model for epistemic evaluation and knowledge          attribution to describe al...
Research Questions:       1. Can we find a model for epistemic evaluation and knowledge          attribution to describe al...
Method:Monday, April 2, 2012
Method:   1.Model for epistemic evaluation?Monday, April 2, 2012
Method:   1.Model for epistemic evaluation?              1.1.Parse text into discourse segments (Elementary Discourse     ...
Method:   1.Model for epistemic evaluation?              1.1.Parse text into discourse segments (Elementary Discourse     ...
Method:   1.Model for epistemic evaluation?              1.1.Parse text into discourse segments (Elementary Discourse     ...
Method:   1.Model for epistemic evaluation?              1.1.Parse text into discourse segments (Elementary Discourse     ...
Method:   1.Model for epistemic evaluation?              1.1.Parse text into discourse segments (Elementary Discourse     ...
Method:   1.Model for epistemic evaluation?              1.1.Parse text into discourse segments (Elementary Discourse     ...
Method:   1.Model for epistemic evaluation?              1.1.Parse text into discourse segments (Elementary Discourse     ...
Method:   1.Model for epistemic evaluation?              1.1.Parse text into discourse segments (Elementary Discourse     ...
Experimental Discourse    Both seminomas and the EC component of    nonseminomas share features with ES cells. To    exclu...
Parsing Experimental Discourse    Both seminomas and the EC component of    nonseminomas share features with ES cells. To ...
Parsing Experimental Discourse    Both seminomas and the EC component of     Both seminomas and the EC component of    non...
Parsing Experimental Discourse    Both seminomas and the EC component of     Both seminomas and the EC component of       ...
Parsing Experimental Discourse    Both seminomas and the EC component of     Both seminomas and the EC component of       ...
Parsing Experimental Discourse    Both seminomas and the EC component of     Both seminomas and the EC component of       ...
Parsing Experimental Discourse    Both seminomas and the EC component of     Both seminomas and the EC component of       ...
Parsing Experimental Discourse    Both seminomas and the EC component of     Both seminomas and the EC component of       ...
Parsing Experimental Discourse    Both seminomas and the EC component of     Both seminomas and the EC component of       ...
Parsing Experimental Discourse    Both seminomas and the EC component of     Both seminomas and the EC component of       ...
Parsing Experimental Discourse                                                                         Conceptual    Both ...
Parsing Experimental Discourse                                                                         Conceptual    Both ...
Segment TypesMonday, April 2, 2012
Segment Types     Segment            Description                          Example     Fact               a known fact, gen...
Segment Types     Segment            Description                          Example     Fact               a known fact, gen...
Segment Types     Segment            Description                          Example     Fact               a known fact, gen...
Realms in scholarly discourse:                              place of hedgingMonday, April 2, 2012
Realms in scholarly discourse:                              place of hedging     (1) Both seminomas        (2) b. the dete...
Realms in scholarly discourse:                                   place of hedging     (1) Both seminomas                  ...
Realms in scholarly discourse:                                    place of hedging     (1) Both seminomas                 ...
Realms in scholarly discourse:                                    place of hedging     (1) Both seminomas                 ...
Realms in scholarly discourse:                                    place of hedging     (1) Both seminomas                 ...
Realms in scholarly discourse:                                    place of hedging                                        ...
Realms in scholarly discourse:                                    place of hedging                                        ...
Realms in scholarly discourse:                                    place of hedging                                        ...
Hedging erosion in actionMonday, April 2, 2012
Hedging erosion in action              To investigate the possibility that             miR-372 and miR-373 suppress the   ...
Hedging erosion in action              To investigate the possibility that             miR-372 and miR-373 suppress the   ...
Hedging erosion in action              To investigate the possibility that             miR-372 and miR-373 suppress the   ...
Hedging erosion in action              To investigate the possibility that             miR-372 and miR-373 suppress the   ...
Hedging erosion in action              To investigate the possibility that             miR-372 and miR-373 suppress the   ...
Hedging erosion in action              To investigate the possibility that             miR-372 and miR-373 suppress the   ...
Hedging erosion in action              To investigate the possibility that             miR-372 and miR-373 suppress the   ...
Hedging erosion in action                                                         Yabuta, JBioChem 2007                   ...
Hedging erosion in action                                                         Yabuta, JBioChem 2007                   ...
Logical structure of epistemic evaluations:Monday, April 2, 2012
Logical structure of epistemic evaluations:       For a Proposition P, an epistemically marked clause E is an       Evalua...
Logical structure of epistemic evaluations:       For a Proposition P, an epistemically marked clause E is an       Evalua...
Some examples:Concept Values                                                   ExampleValue                   0 - Lack of ...
Epistemic MarkersMonday, April 2, 2012
Epistemic Markers  -       Modal auxiliary verbs (e.g. can, could, might)Monday, April 2, 2012
Epistemic Markers  -       Modal auxiliary verbs (e.g. can, could, might)  -       Qualifying adverbs and adjectives (e.g....
Epistemic Markers  -       Modal auxiliary verbs (e.g. can, could, might)  -       Qualifying adverbs and adjectives (e.g....
Epistemic Markers  -       Modal auxiliary verbs (e.g. can, could, might)  -       Qualifying adverbs and adjectives (e.g....
Markers v. Types: 1 paper, 640 segments   Value                    Modal       Reporting Ruled      Adverbs/ Referen None ...
Markers v. Types: 1 paper, 640 segments   Value                    Modal       Reporting Ruled      Adverbs/ Referen None ...
Markers v. Types: 1 paper, 640 segments   Value                    Modal       Reporting Ruled      Adverbs/ Referen None ...
Markers v. Types: 1 paper, 640 segments   Value                    Modal       Reporting Ruled      Adverbs/ Referen None ...
Reporting verbs vs. epistemic value:Monday, April 2, 2012
Reporting verbs vs. epistemic value:     Value = 0                establish, (remain to be) elucidated,     (unknown)     ...
Most prevalent clause type:                        “These results suggest that...”Monday, April 2, 2012
Most prevalent clause type:                        “These results suggest that...”    Adverb/Connective       thus, theref...
Can we find this automatically?                        ‘Claimed knowledge updates’:                                        ...
Preliminary steps towards                                          citation analysis:  Type                  Voorhoeve tex...
Conclusions:Monday, April 2, 2012
Conclusions: 1. Can we find a model for epistemic evaluation and knowledge attribution    to describe all biological statem...
Conclusions: 1. Can we find a model for epistemic evaluation and knowledge attribution    to describe all biological statem...
Conclusions: 1. Can we find a model for epistemic evaluation and knowledge attribution    to describe all biological statem...
Next steps:Monday, April 2, 2012
Next steps:   1. Co-annotator validation of epistemic mark up: do we all agree on what      (the author says) is true, pro...
Next steps:   1. Co-annotator validation of epistemic mark up: do we all agree on what      (the author says) is true, pro...
Next steps:   1. Co-annotator validation of epistemic mark up: do we all agree on what      (the author says) is true, pro...
Acknowledgements:               Collaborators:               - Henk Pander Maat, Universiteit Utrecht               - Agne...
Tense and MythologyMonday, April 2, 2012
Recursion/patterns of rhetoric:                        Main moves in an experimental paperMonday, April 2, 2012
Recursion/patterns of rhetoric:                        Main moves in an experimental paper                           Facts...
Recursion/patterns of rhetoric:                        Main moves in an experimental paper                           Facts...
Recursion/patterns of rhetoric:                        Main moves in an experimental paper                           Facts...
Recursion/patterns of rhetoric:                        Main moves in an experimental paper                           Facts...
Recursion/patterns of rhetoric:                        Main moves in an experimental paper                           Facts...
Recursion/patterns of rhetoric:                        Main moves in an experimental paper                           Facts...
Recursion/patterns of rhetoric:                        Main moves in an experimental paper                           Facts...
Recursion/patterns of rhetoric:                        Main moves in an experimental paper                           Facts...
Mechanisms for realm transitionsMonday, April 2, 2012
Mechanisms for realm transitions -       Verb form change: -       Goal transitions: -       Regulatory segments:Monday, A...
Mechanisms for realm transitions -       Verb form change:          Whereas all three cluster-expressing cell lines contai...
Mechanisms for realm transitions -       Verb form change:          Whereas all three cluster-expressing cell lines contai...
Mechanisms for realm transitions -       Verb form change:          Whereas all three cluster-expressing cell lines contai...
Sentence-initial adverbials?Monday, April 2, 2012
Sentence-initial adverbials?       -       Not relevant for realm transitions:       -       Relevant for realm transition...
Sentence-initial adverbials?       -       Not relevant for realm transitions:        Furthermore, we confirmed the consis...
Sentence-initial adverbials?       -       Not relevant for realm transitions:        Furthermore, we confirmed the consis...
More general: verb form as realm indicatorMonday, April 2, 2012
More general: verb form as realm indicator                    -   Conceptual realm: ‘state’ (gnomic) present              ...
More general: verb form as realm indicator                    -   Conceptual realm: ‘state’ (gnomic) present              ...
More general: verb form as realm indicator                    -   Conceptual realm: ‘state’ (gnomic) present              ...
More general: verb form as realm indicator                    -   Conceptual realm: ‘state’ (gnomic) present              ...
More general: verb form as realm indicator                    -   Conceptual realm: ‘state’ (gnomic) present              ...
‘Referring Use of Tense’                                                   FutureMonday, April 2, 2012
‘Referring Use of Tense’                               Concepts                             ‘Gnomic’ present              ...
‘Referring Use of Tense’                               Concepts                             ‘Gnomic’ present              ...
‘Referring Use of Tense’                               Concepts                             ‘Gnomic’ present              ...
‘Referring Use of Tense’                               Concepts                             ‘Gnomic’ present              ...
‘Referring Use of Tense’                               Concepts                             ‘Gnomic’ present              ...
‘Referring Use of Tense’                               Concepts                             ‘Gnomic’ present              ...
Anecdotal excursion into mythological text:Monday, April 2, 2012
Anecdotal excursion into mythological text:Facts in the            Endogenous small RNAs (miRNAs)                   I sing...
Anecdotal excursion into mythological text:Facts in the            Endogenous small RNAs (miRNAs)                   I sing...
Anecdotal excursion into mythological text:Facts in the            Endogenous small RNAs (miRNAs)                   I sing...
Anecdotal excursion into mythological text:Facts in the            Endogenous small RNAs (miRNAs)                   I sing...
Anecdotal excursion into mythological text:Facts in the            Endogenous small RNAs (miRNAs)                   I sing...
Realms and planes: Patterns and Blends                                     Concepts                                      ‘...
Realms and planes: Patterns and Blends                                     Concepts                                      ‘...
'These Results Suggest That...', Knowledge Attribution in Scientific Discourse
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Talk on Epistemic Modality Modelling for dept of linguistics, University of Lethbridge, Lethbridge, Alberta

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'These Results Suggest That...', Knowledge Attribution in Scientific Discourse

  1. 1. ‘These results suggest that...’ Knowledge Attribution in Scientific Discourse Anita de Waard Disruptive Technologies Director, Elsevier Labs Casimir Researcher, University of Utrecht University of Lethbridge, April 2 2012Monday, April 2, 2012
  2. 2. How a claim becomes a fact: - Voorhoeve, 2006: “These miRNAs neutralize p53- mediated CDK inhibition, possibly through direct inhibition of the expression of the tumorsuppressor LATS2.” - Kloosterman and Plasterk, 2006: “In a genetic screen, miR-372 and miR-373 were found to allow proliferation of primary human cells that express oncogenic RAS and active p53, possibly by inhibiting the tumor suppressor LATS2 (Voorhoeve et al., 2006).” - Yabuta et al., 2007: “[On the other hand,] two miRNAs, miRNA-372 and-373, function as potential novel oncogenes in testicular germ cell tumors by inhibition of LATS2 expression, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).” - Okada et al., 2011: “Two oncogenic miRNAs, miR-372 and miR-373, directly inhibit the expression of Lats2, thereby allowing tumorigenic growth in the presence of p53 (Voorhoeve et al., 2006).”Monday, April 2, 2012
  3. 3. “[Y]ou can transform a fact into fiction or a fiction into fact just by adding or subtracting references [and data]” – Bruno Latour, ‘Science in Action’,1987 Text TextMonday, April 2, 2012
  4. 4. “[Y]ou can transform a fact into fiction or a fiction into fact just by adding or subtracting references [and data]” – Bruno Latour, ‘Science in Action’,1987 Text TextMonday, April 2, 2012
  5. 5. Research Questions:Monday, April 2, 2012
  6. 6. Research Questions: 1. Can we find a model for epistemic evaluation and knowledge attribution to describe all biological statements in a straightforward way?Monday, April 2, 2012
  7. 7. Research Questions: 1. Can we find a model for epistemic evaluation and knowledge attribution to describe all biological statements in a straightforward way? 2. If yes: can we detect this evaluation - manually, and automatically?Monday, April 2, 2012
  8. 8. Research Questions: 1. Can we find a model for epistemic evaluation and knowledge attribution to describe all biological statements in a straightforward way? 2. If yes: can we detect this evaluation - manually, and automatically? 3. Is this model useful for examining the mechanism of ‘hedging erosion’, does it show how a claim becomes validated after being cited?Monday, April 2, 2012
  9. 9. Method:Monday, April 2, 2012
  10. 10. Method: 1.Model for epistemic evaluation?Monday, April 2, 2012
  11. 11. Method: 1.Model for epistemic evaluation? 1.1.Parse text into discourse segments (Elementary Discourse Units) containing a single rhetorical move (roughly, a clause)Monday, April 2, 2012
  12. 12. Method: 1.Model for epistemic evaluation? 1.1.Parse text into discourse segments (Elementary Discourse Units) containing a single rhetorical move (roughly, a clause) 1.2.Identify levels of epistemic evaluationMonday, April 2, 2012
  13. 13. Method: 1.Model for epistemic evaluation? 1.1.Parse text into discourse segments (Elementary Discourse Units) containing a single rhetorical move (roughly, a clause) 1.2.Identify levels of epistemic evaluation 1.3.Do a co-annotator study to see if these levels are sharedMonday, April 2, 2012
  14. 14. Method: 1.Model for epistemic evaluation? 1.1.Parse text into discourse segments (Elementary Discourse Units) containing a single rhetorical move (roughly, a clause) 1.2.Identify levels of epistemic evaluation 1.3.Do a co-annotator study to see if these levels are shared 2. How to detect?Monday, April 2, 2012
  15. 15. Method: 1.Model for epistemic evaluation? 1.1.Parse text into discourse segments (Elementary Discourse Units) containing a single rhetorical move (roughly, a clause) 1.2.Identify levels of epistemic evaluation 1.3.Do a co-annotator study to see if these levels are shared 2. How to detect? 2.1.Identify markers of epistemic evaluation/knowledge attributionMonday, April 2, 2012
  16. 16. Method: 1.Model for epistemic evaluation? 1.1.Parse text into discourse segments (Elementary Discourse Units) containing a single rhetorical move (roughly, a clause) 1.2.Identify levels of epistemic evaluation 1.3.Do a co-annotator study to see if these levels are shared 2. How to detect? 2.1.Identify markers of epistemic evaluation/knowledge attribution 2.2.Work with computational linguists to see if these can be found automaticallyMonday, April 2, 2012
  17. 17. Method: 1.Model for epistemic evaluation? 1.1.Parse text into discourse segments (Elementary Discourse Units) containing a single rhetorical move (roughly, a clause) 1.2.Identify levels of epistemic evaluation 1.3.Do a co-annotator study to see if these levels are shared 2. How to detect? 2.1.Identify markers of epistemic evaluation/knowledge attribution 2.2.Work with computational linguists to see if these can be found automatically 3. Useful for hedging erosion?Monday, April 2, 2012
  18. 18. Method: 1.Model for epistemic evaluation? 1.1.Parse text into discourse segments (Elementary Discourse Units) containing a single rhetorical move (roughly, a clause) 1.2.Identify levels of epistemic evaluation 1.3.Do a co-annotator study to see if these levels are shared 2. How to detect? 2.1.Identify markers of epistemic evaluation/knowledge attribution 2.2.Work with computational linguists to see if these can be found automatically 3. Useful for hedging erosion? 3.1.Perform a diachronic study of citation evaluationMonday, April 2, 2012
  19. 19. Experimental Discourse 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.Monday, April 2, 2012
  20. 20. Parsing Experimental Discourse 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.Monday, April 2, 2012
  21. 21. Parsing Experimental Discourse 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.Monday, April 2, 2012
  22. 22. Parsing Experimental Discourse 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.Monday, April 2, 2012
  23. 23. Parsing Experimental Discourse 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.Monday, April 2, 2012
  24. 24. Parsing Experimental Discourse 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.Monday, April 2, 2012
  25. 25. Parsing Experimental Discourse 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.Monday, April 2, 2012
  26. 26. Parsing Experimental Discourse 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.Monday, April 2, 2012
  27. 27. Parsing Experimental Discourse 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.Monday, April 2, 2012
  28. 28. Parsing Experimental Discourse 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.Monday, April 2, 2012
  29. 29. Parsing Experimental Discourse 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.Monday, April 2, 2012
  30. 30. Parsing Experimental Discourse 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.Monday, April 2, 2012
  31. 31. Segment TypesMonday, April 2, 2012
  32. 32. Segment Types Segment Description Example Fact a known fact, generally without mature miR-373 is a homolog of miR-372 explicit citation Hypothesis a proposed idea, not supported by This could for instance be a result of high 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, in our procedure is sensitive enough to detect light of earlier hypotheses and facts mild growth differencesMonday, April 2, 2012
  33. 33. Segment Types Segment Description Example Fact a known fact, generally without mature miR-373 is a homolog of miR-372 explicit citation Hypothesis a proposed idea, not supported by This could for instance be a result of high 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, in our procedure is sensitive enough to detect light of earlier hypotheses and facts mild growth differences ‘Other-segments’, related to (referenced) other work - e.g. with referenceMonday, April 2, 2012
  34. 34. Segment Types Segment Description Example Fact a known fact, generally without mature miR-373 is a homolog of miR-372 explicit citation Hypothesis a proposed idea, not supported by This could for instance be a result of high 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, in our procedure is sensitive enough to detect light of earlier hypotheses and facts mild growth differences ‘Other-segments’, related to (referenced) other work - e.g. with reference Regulatory segments, acting as matrix sentences framing other segments, ‘Altogether, this suggests that’Monday, April 2, 2012
  35. 35. Realms in scholarly discourse: place of hedgingMonday, April 2, 2012
  36. 36. Realms in scholarly discourse: place of hedging (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,Monday, April 2, 2012
  37. 37. Realms in scholarly discourse: place of hedging (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 thatMonday, April 2, 2012
  38. 38. Realms in scholarly discourse: place of hedging (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),Monday, April 2, 2012
  39. 39. Realms in scholarly discourse: place of hedging (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 (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),Monday, April 2, 2012
  40. 40. Realms in scholarly discourse: place of hedging (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 (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),Monday, April 2, 2012
  41. 41. Realms in scholarly discourse: place of hedging 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 (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),Monday, April 2, 2012
  42. 42. Realms in scholarly discourse: place of hedging 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 (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), ExperimentMonday, April 2, 2012
  43. 43. Realms in scholarly discourse: place of hedging 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 (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), ExperimentMonday, April 2, 2012
  44. 44. Hedging erosion in actionMonday, April 2, 2012
  45. 45. Hedging erosion in action To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we... HypothesisMonday, April 2, 2012
  46. 46. Hedging erosion in action To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we... KnownFact KnownFact Concepts HypothesisMonday, April 2, 2012
  47. 47. Hedging erosion in action To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we... KnownFact KnownFact Concepts Hypothesis Goal Method Result Data Experiment 1Monday, April 2, 2012
  48. 48. Hedging erosion in action To investigate the possibility that miR-372 and miR-373 suppress the expression of LATS2, we... Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity, KnownFact KnownFact Concepts Hypothesis Implication Goal Method Result Data Experiment 1Monday, April 2, 2012
  49. 49. Hedging erosion in action To investigate the possibility that miR-372 and miR-373 suppress the Voorhoeve, 2006 expression of LATS2, we... Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity, KnownFact KnownFact Concepts Hypothesis Implication Goal Method Result Data Experiment 1Monday, April 2, 2012
  50. 50. Hedging erosion in action To investigate the possibility that miR-372 and miR-373 suppress the Voorhoeve, 2006 expression of LATS2, we... Therefore, these results point to LATS2 as a mediator of the miR-372 and miR-373 effects on cell proliferation and tumorigenicity, KnownFact KnownFact Concepts Hypothesis Implication Goal Goal Method Result Method Result Data Data Experiment 1 Experiment 2Monday, April 2, 2012
  51. 51. Hedging erosion in action To investigate the possibility that miR-372 and miR-373 suppress the Voorhoeve, 2006 expression of LATS2, we... Raver-Shapira et.al, JMolCell 2007 Therefore, these results point to two miRNAs, miRNA-372 and-373, function as LATS2 as a mediator of the miR-372 and potential novel oncogenes in testicular germ miR-373 effects on cell proliferation and cell tumors by inhibition of LATS2 expression, tumorigenicity, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006). KnownFact KnownFact Concepts Hypothesis Implication Fact Goal Goal Method Result Method Result Data Data Experiment 1 Experiment 2Monday, April 2, 2012
  52. 52. Hedging erosion in action Yabuta, JBioChem 2007 miR-372 and miR-373 target the To investigate the possibility that miR-372 and miR-373 suppress the Voorhoeve, 2006 Lats2 tumor suppressor (Voorhoeve et al., 2006) expression of LATS2, we... Raver-Shapira et.al, JMolCell 2007 Therefore, these results point to two miRNAs, miRNA-372 and-373, function as LATS2 as a mediator of the miR-372 and potential novel oncogenes in testicular germ miR-373 effects on cell proliferation and cell tumors by inhibition of LATS2 expression, tumorigenicity, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006). KnownFact KnownFact Concepts Hypothesis Implication Fact Goal Goal Method Result Method Result Data Data Experiment 1 Experiment 2Monday, April 2, 2012
  53. 53. Hedging erosion in action Yabuta, JBioChem 2007 miR-372 and miR-373 target the To investigate the possibility that miR-372 and miR-373 suppress the Voorhoeve, 2006 Lats2 tumor suppressor (Voorhoeve et al., 2006) expression of LATS2, we... Raver-Shapira et.al, JMolCell 2007 Therefore, these results point to two miRNAs, miRNA-372 and-373, function as LATS2 as a mediator of the miR-372 and potential novel oncogenes in testicular germ miR-373 effects on cell proliferation and cell tumors by inhibition of LATS2 expression, tumorigenicity, which suggests that Lats2 is an important tumor suppressor (Voorhoeve et al., 2006). KnownFact KnownFact Concepts Hypothesis Implication Fact Goal Goal Method Result Method Result Data Data Experiment 1 Experiment 2 http://elsatglabs.com/labs/anita/demos/LATSDemo102007/Monday, April 2, 2012
  54. 54. Logical structure of epistemic evaluations:Monday, April 2, 2012
  55. 55. Logical structure of epistemic evaluations: For a Proposition P, an epistemically marked clause E is an Evaluation of P, EV, B, S(P), with: - V = Value: 3 = Assumed true, 2 = Probable, 1 = Possible, 0 = Unknown, (- 1= possibly untrue, - 2 = probably untrue, -3 = assumed untrue) - B = Basis: Reasoning Data - S = Source: A = speaker is author A, explicit IA = speaker author, A, implicit N = other author N, explicit NN = other author NN, implicitMonday, April 2, 2012
  56. 56. Logical structure of epistemic evaluations: For a Proposition P, an epistemically marked clause E is an Evaluation of P, EV, B, S(P), with: - V = Value: 3 = Assumed true, 2 = Probable, 1 = Possible, 0 = Unknown, (- 1= possibly untrue, - 2 = probably untrue, -3 = assumed untrue) - B = Basis: Reasoning Data - S = Source: A = speaker is author A, explicit IA = speaker author, A, implicit N = other author N, explicit NN = other author NN, implicit Model suggested by Eduard Hovy, Information Sciences Institute University South CaliformiaMonday, April 2, 2012
  57. 57. Some examples:Concept Values ExampleValue 0 - Lack of knowledge: Thus, it remains to be determined if... 1 – Hypothetical: low certainty GATA-1 binding to exon 1 may affect transcription start site function 2 – Dubitative: higher likelihood but suggesting the presence of lineage-specific elements. short of complete certainty 3 – Doxastic: complete certainty, the 1.6 kb 5 flanking region of CCR3 has promoter accepted/known/proven fact activity in vivo.Basis R – Reasoning Therefore, one can argue…’ D – Data These results suggest…’ 0 – Unidentified Studies report that…’Source A - Author: Explicit mention of We hypothesize that…’; ‘Figure 2a shows that… author/speaker or current paper as source N - Named external source, either …several reports have documented this expression explicitly or as a reference [11-16,42]. IA - Implicit attribution to the author Electrophoretic mobility shift analysis revealed that… NN – Nameless external source no eosinophil-specific transcription factors have been reported… 0 – No source of knowledge transcription factors are the final common pathway driving differentiationMonday, April 2, 2012
  58. 58. Epistemic MarkersMonday, April 2, 2012
  59. 59. Epistemic Markers - Modal auxiliary verbs (e.g. can, could, might)Monday, April 2, 2012
  60. 60. Epistemic Markers - Modal auxiliary verbs (e.g. can, could, might) - Qualifying adverbs and adjectives (e.g. interestingly, possibly, likely, potential, somewhat, slightly, powerful, unknown, undefined)Monday, April 2, 2012
  61. 61. Epistemic Markers - Modal auxiliary verbs (e.g. can, could, might) - Qualifying adverbs and adjectives (e.g. interestingly, possibly, likely, potential, somewhat, slightly, powerful, unknown, undefined) - References, either external (e.g. ‘[Voorhoeve et al., 2006]’) or internal (e.g. ‘See fig. 2a’).Monday, April 2, 2012
  62. 62. Epistemic Markers - Modal auxiliary verbs (e.g. can, could, might) - Qualifying adverbs and adjectives (e.g. interestingly, possibly, likely, potential, somewhat, slightly, powerful, unknown, undefined) - References, either external (e.g. ‘[Voorhoeve et al., 2006]’) or internal (e.g. ‘See fig. 2a’). - Reporting/epistemic verbs (e.g. suggest, imply, indicate, show) - either within the clause: ‘These results suggest that...’ - or in a subordinate clause governed by reporting-verb matrix clause ‘{These results suggest that} indeed, this represents the true endogenous activity.’Monday, April 2, 2012
  63. 63. Markers v. Types: 1 paper, 640 segments Value Modal Reporting Ruled Adverbs/ Referen None Total Aux Verb by RV Adjectiv ces es Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%) Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%) Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%) Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%) Total No 16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%) Modality Overall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)Monday, April 2, 2012
  64. 64. Markers v. Types: 1 paper, 640 segments Value Modal Reporting Ruled Adverbs/ Referen None Total Aux Verb by RV Adjectiv ces es Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%) Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%) Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%) Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%) Total No 16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%) Modality Overall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)Monday, April 2, 2012
  65. 65. Markers v. Types: 1 paper, 640 segments Value Modal Reporting Ruled Adverbs/ Referen None Total Aux Verb by RV Adjectiv ces es Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%) Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%) Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%) Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%) Total No 16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%) Modality Overall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)Monday, April 2, 2012
  66. 66. Markers v. Types: 1 paper, 640 segments Value Modal Reporting Ruled Adverbs/ Referen None Total Aux Verb by RV Adjectiv ces es Total value = 3 1 (0.5%) 81 (40%) 24 (12%) 7 (4%) 41 (20%) 47 (24%) 201(100%) Total Value = 2 29 (51%) 23 (40%) 1 (2%) 4(7%) 57(100%) Total Value = 1 9(27%) 11(33%) 11(33%) 1(3%) 1(3%) 33(100%) Total Value = 0 9 (64%) 3 (21%) 1(7%) 1(7%) 14(100%) Total No 16(37%) 3(7%) 0 3(7%) 22(50%) 44(100%) Modality Overall Total 10 (2%) 146(23%) 64(10%) 10(2%) 50(8%) 69(11%) 640(100%)Monday, April 2, 2012
  67. 67. Reporting verbs vs. epistemic value:Monday, April 2, 2012
  68. 68. Reporting verbs vs. epistemic value: Value = 0 establish, (remain to be) elucidated, (unknown) be (clear/useful), (remain to be) examined/determined, describe, make difficult to infer, report Value = 1 be important, consider, expect, hypothesize (5x), (hypothetical) give insight, raise possibility that, suspect, think Value = 2 appear, believe, implicate (2x), imply, indicate (12x), (probable) play a role, represent, suggest (18x), validate (2x), Value = 3 be able/apparent/important /positive/visible, compare (presumed true) (2x), confirm (2x), define, demonstrate (15x), detect (5x), discover, display (3x), eliminate, find (3x), identify (4x), know, need, note (2x), observe (2x), obtain (success/results- 3x), prove to be, refer, report(2x), reveal (3x), see(2x), show(24x), study, viewMonday, April 2, 2012
  69. 69. Most prevalent clause type: “These results suggest that...”Monday, April 2, 2012
  70. 70. Most prevalent clause type: “These results suggest that...” Adverb/Connective thus, therefore, together, recently, in summary Determiner/Pronoun it, this, these, we/our Adjective previous, future, better Noun phrase data, report, study, result(s); method or reference Modal form of ‘to be’, may, remain Adjective often, recently, generally Verb show, obtain, consider, view, reveal, suggest, hypothesize, indicate, believe Preposition that, toMonday, April 2, 2012
  71. 71. Can we find this automatically? ‘Claimed knowledge updates’: Work done with Agnes Sandor, Xerox Research EuropeMonday, April 2, 2012
  72. 72. Preliminary steps towards citation analysis: Type Voorhoeve text Citing text Method We subsequently created a human Voorhoeve et al. (116) employed a novel strategy by miRNA expression library (miR-Lib) combining an miRNA vector library and corresponding by cloning almost all annotated bar code array Using a novel retroviral miRNA human miRNAs into our vector expression library, (Rfam release 6) (Figure S3) Agami and co-workers performed a cell-based screen Result we identified miR-372 and miR-372 and miR-373 were consequently found to permit miR-373, each permitting proliferation and tumorigenesis of these primary cells proliferation and tumorigenesis carrying both oncogenic RAS and wild-type p53, of primary human cells that Voorhoeve et al. (2006) identified miR-372 and miR-373 harbor both oncogenic RAS miR-372 has been recently described as potential and active wild - type p53. oncogene that collaborate with oncogenic RAS in cellular transformation Interpretat These miRNAs neutralize p53- probably through direct inhibition of the expression of the ion mediated CDK inhibition, tumor-suppressor LATS2 and subsequent neutralization possibly through direct of the p53 pathway. inhibition of the expression of Compromised Lats2 functionality might reduce the the tumor suppressor LATS2 . selective pressure for p53 inactivation during tumor progressionRas activation. Work done with Lucy Vanderwende, Microsoft ResearchMonday, April 2, 2012
  73. 73. Conclusions:Monday, April 2, 2012
  74. 74. Conclusions: 1. Can we find a model for epistemic evaluation and knowledge attribution to describe all biological statements in a straightforward way? - Yes: three-dimensional model - Value, Basis, Source; - Four markers: modal auxiliaries, adverbs, references, reporting verbs; - Correlation: reporting verbs + that = most prevalent marker; value = 1: modal aux; value = 0: phrase; value = 3: refs or noneMonday, April 2, 2012
  75. 75. Conclusions: 1. Can we find a model for epistemic evaluation and knowledge attribution to describe all biological statements in a straightforward way? - Yes: three-dimensional model - Value, Basis, Source; - Four markers: modal auxiliaries, adverbs, references, reporting verbs; - Correlation: reporting verbs + that = most prevalent marker; value = 1: modal aux; value = 0: phrase; value = 3: refs or none 2. If yes: can we detect this evaluation automatically? - Early results are promising, needs more validationMonday, April 2, 2012
  76. 76. Conclusions: 1. Can we find a model for epistemic evaluation and knowledge attribution to describe all biological statements in a straightforward way? - Yes: three-dimensional model - Value, Basis, Source; - Four markers: modal auxiliaries, adverbs, references, reporting verbs; - Correlation: reporting verbs + that = most prevalent marker; value = 1: modal aux; value = 0: phrase; value = 3: refs or none 2. If yes: can we detect this evaluation automatically? - Early results are promising, needs more validation 3. Is this model useful for examining the mechanism of ‘hedging erosion’, does it show how a claim becomes validated after being cited? - Probably! More work to be done...Monday, April 2, 2012
  77. 77. Next steps:Monday, April 2, 2012
  78. 78. Next steps: 1. Co-annotator validation of epistemic mark up: do we all agree on what (the author says) is true, probable, possible, unknown?Monday, April 2, 2012
  79. 79. Next steps: 1. Co-annotator validation of epistemic mark up: do we all agree on what (the author says) is true, probable, possible, unknown? 2. Full-blown diachronic study: statistical validation for this trend?Monday, April 2, 2012
  80. 80. Next steps: 1. Co-annotator validation of epistemic mark up: do we all agree on what (the author says) is true, probable, possible, unknown? 2. Full-blown diachronic study: statistical validation for this trend? 3. Work with bioinformaticians: - (Make OWL ontology) and add to formal knowledge representations, e.g. Biological Expression Language add {V = 3, S = N, B = 0}: - SET Evidence = "Arterial cells are highly susceptible to oxidative stress, which can induce both necrosis and apoptosis (programmed cell death) [1,2]" - biologicalProcess(GO:"response to oxidative stress") increases biologicalProcess (GO:"apoptotic process") - biologicalProcess(GO:"response to oxidative stress") increases biologicalProcess (GO:necrosis) - Improve triple search engines, e.g. compare in iHop: - The Lats2 tumor suppressor protein has been implicated earlier in promoting p53 activation in response to mitotic apparatus stress {V = 2, S = NN, B = 0} - Our findings reveal that miR-373 would be a potential oncogene and it participates in the carcinogenesis of human esophageal cancer {V = 1/2?, S = A, B = D}Monday, April 2, 2012
  81. 81. Acknowledgements: Collaborators: - Henk Pander Maat, Universiteit Utrecht - Agnes Sandor, Xerox Research Europe - Lucy Vanderwende, Microsoft Research - Eduard H. Hovy, USC Information Sciences Institute - Dexter Pratt, Biological Exchange Language Funding: - NWO/Casimir Subsidy, 2006-2010 - 2010+ - Elsevier Labs Anita de Waard, a.dewaard@elsevier.com http://elsatglabs.com/labs/anitaMonday, April 2, 2012
  82. 82. Tense and MythologyMonday, April 2, 2012
  83. 83. Recursion/patterns of rhetoric: Main moves in an experimental paperMonday, April 2, 2012
  84. 84. Recursion/patterns of rhetoric: Main moves in an experimental paper Facts Problem HypothesisMonday, April 2, 2012
  85. 85. Recursion/patterns of rhetoric: Main moves in an experimental paper Facts Problem Hypothesis GoalMonday, April 2, 2012
  86. 86. Recursion/patterns of rhetoric: Main moves in an experimental paper Facts Problem Hypothesis Goal Method ResultsMonday, April 2, 2012
  87. 87. Recursion/patterns of rhetoric: Main moves in an experimental paper Facts Problem Hypothesis Goal These results suggest that.... Method ResultsMonday, April 2, 2012
  88. 88. Recursion/patterns of rhetoric: Main moves in an experimental paper Facts Problem Implication Hypothesis Goal These results suggest that.... Method ResultsMonday, April 2, 2012
  89. 89. Recursion/patterns of rhetoric: Main moves in an experimental paper Facts Concepts Problem Implication Hypothesis Goal These results suggest that.... Method ResultsMonday, April 2, 2012
  90. 90. Recursion/patterns of rhetoric: Main moves in an experimental paper Facts Concepts Problem Implication Hypothesis Goal These results suggest that.... Method Experiment ResultsMonday, April 2, 2012
  91. 91. Recursion/patterns of rhetoric: Main moves in an experimental paper Facts Concepts Problem Implication Hypothesis Transitions Goal These results suggest that.... Method Experiment ResultsMonday, April 2, 2012
  92. 92. Mechanisms for realm transitionsMonday, April 2, 2012
  93. 93. Mechanisms for realm transitions - Verb form change: - Goal transitions: - Regulatory segments:Monday, April 2, 2012
  94. 94. Mechanisms for realm transitions - Verb form change: Whereas all three cluster-expressing cell lines contained high wt-p53 levels, NTera2 has low wild-type p53 levels, and NCCIT lost one p53 allele while the second allele is mutated (Burger et al, 1998). - Goal transitions: - Regulatory segments:Monday, April 2, 2012
  95. 95. Mechanisms for realm transitions - Verb form change: Whereas all three cluster-expressing cell lines contained high wt-p53 levels, NTera2 has low wild-type p53 levels, and NCCIT lost one p53 allele while the second allele is mutated (Burger et al, 1998). - Goal transitions: 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... - Regulatory segments:Monday, April 2, 2012
  96. 96. Mechanisms for realm transitions - Verb form change: Whereas all three cluster-expressing cell lines contained high wt-p53 levels, NTera2 has low wild-type p53 levels, and NCCIT lost one p53 allele while the second allele is mutated (Burger et al, 1998). - Goal transitions: 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... - Regulatory segments: 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).Monday, April 2, 2012
  97. 97. Sentence-initial adverbials?Monday, April 2, 2012
  98. 98. Sentence-initial adverbials? - Not relevant for realm transitions: - Relevant for realm transition?Monday, April 2, 2012
  99. 99. Sentence-initial adverbials? - Not relevant for realm transitions: Furthermore, we confirmed the consistency of miRNA expression driven by miRVec by cloning eight miR-Vec plasmids expressing randomly chosen miRNAs. With one exception, all constructs yielded high expression levels of mature miRNAs (Figure S1). Notably, very little pre-miRNA accumulation was detected in all cases, indicating the efficient processing of the ectopically expressed miRNAs in the cells. - Relevant for realm transition?Monday, April 2, 2012
  100. 100. Sentence-initial adverbials? - Not relevant for realm transitions: Furthermore, we confirmed the consistency of miRNA expression driven by miRVec by cloning eight miR-Vec plasmids expressing randomly chosen miRNAs. With one exception, all constructs yielded high expression levels of mature miRNAs (Figure S1). Notably, very little pre-miRNA accumulation was detected in all cases, indicating the efficient processing of the ectopically expressed miRNAs in the cells. -The third constructrealm transition? miR-Vec-371&2 Relevant for did not overlap with and encoded miRNA-373 and 373*. Interestingly, the mature miR-373 is a homolog of miR-372, and neither shares obvious homology with either miRNA-371 or miR-373* (Fig.2D).Monday, April 2, 2012
  101. 101. More general: verb form as realm indicatorMonday, April 2, 2012
  102. 102. More general: verb form as realm indicator - Conceptual realm: ‘state’ (gnomic) present ‘Dopaminergic innervation plays a major role in the control of mood and its perturbation’Monday, April 2, 2012
  103. 103. More general: verb form as realm indicator - Conceptual realm: ‘state’ (gnomic) present ‘Dopaminergic innervation plays a major role in the control of mood and its perturbation’ - Experimental realm: ‘event’ past ‘Four out of seven cell lines expressed this cluster’, ‘Adult rats were individually housed for 2 days before testing.’Monday, April 2, 2012
  104. 104. More general: verb form as realm indicator - Conceptual realm: ‘state’ (gnomic) present ‘Dopaminergic innervation plays a major role in the control of mood and its perturbation’ - Experimental realm: ‘event’ past ‘Four out of seven cell lines expressed this cluster’, ‘Adult rats were individually housed for 2 days before testing.’ - Argumentational realm: ‘instantaneous’ present; to-infinitive ‘These results suggest that...’, ‘To identify...’Monday, April 2, 2012
  105. 105. More general: verb form as realm indicator - Conceptual realm: ‘state’ (gnomic) present ‘Dopaminergic innervation plays a major role in the control of mood and its perturbation’ - Experimental realm: ‘event’ past ‘Four out of seven cell lines expressed this cluster’, ‘Adult rats were individually housed for 2 days before testing.’ - Argumentational realm: ‘instantaneous’ present; to-infinitive ‘These results suggest that...’, ‘To identify...’ - Discourse progression: ‘instantaneous’ present ‘Fig 2a shows that’, ‘see figure 7A’,Monday, April 2, 2012
  106. 106. More general: verb form as realm indicator - Conceptual realm: ‘state’ (gnomic) present ‘Dopaminergic innervation plays a major role in the control of mood and its perturbation’ - Experimental realm: ‘event’ past ‘Four out of seven cell lines expressed this cluster’, ‘Adult rats were individually housed for 2 days before testing.’ - Argumentational realm: ‘instantaneous’ present; to-infinitive ‘These results suggest that...’, ‘To identify...’ - Discourse progression: ‘instantaneous’ present ‘Fig 2a shows that’, ‘see figure 7A’, - Reference to other work: present perfect - ‘finalised’ past ‘Previous work has demonstrated that VPCs are sensitive to the levels of let-60/RAS (Han and Sternberg, 1990).’Monday, April 2, 2012
  107. 107. ‘Referring Use of Tense’ FutureMonday, April 2, 2012
  108. 108. ‘Referring Use of Tense’ Concepts ‘Gnomic’ present FutureMonday, April 2, 2012
  109. 109. ‘Referring Use of Tense’ Concepts ‘Gnomic’ present Future Experiment Event pastMonday, April 2, 2012
  110. 110. ‘Referring Use of Tense’ Concepts ‘Gnomic’ present Argumentation: Instantaneous present/To-inf Future Experiment Event pastMonday, April 2, 2012
  111. 111. ‘Referring Use of Tense’ Concepts ‘Gnomic’ present Argumentation: Instantaneous present/To-inf Discourse progression Future Instantaneous present Experiment Event pastMonday, April 2, 2012
  112. 112. ‘Referring Use of Tense’ Concepts ‘Gnomic’ present Argumentation: Instantaneous present/To-inf Other/Past Work Discourse Present progression Future Instantaneous present Experiment Event pastMonday, April 2, 2012
  113. 113. ‘Referring Use of Tense’ Concepts ‘Gnomic’ present Argumentation: Instantaneous present/To-inf Other/Past Future Work Discourse Work Present progression Future Instantaneous present Experiment Event pastMonday, April 2, 2012
  114. 114. Anecdotal excursion into mythological text:Monday, April 2, 2012
  115. 115. Anecdotal excursion into mythological text:Facts in the Endogenous small RNAs (miRNAs) I sing of golden-throned Hera whom Rheaeternal regulate gene expression by mechanisms bare. Queen of the immortals is she, surpassing conserved across metazoans. all in beauty: she is the sister and the wife ofpresent: 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 tosimple past: time investigating a juvenile in the first and gladsome song, and made them merry, and second sessions in experiments conducted in waited till evening should come; and as they the NAC and the striatum: T1 values were made merry dark evening came upon them. 122 ± 6 s and 114 ± 5 s.Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped withembedded the RASV12-ERTAM chimera gene, which sharp bronze, heavy and huge and strong, is only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-offacts: Vita et al, 2005). warriors, with whom she is wroth, she, the daughter of the mighty sire.Attribution in miRNAs have emerged as important In this book I have had old stories writtenthe present regulators of development and control down, as I have heard them told by intelligent processes such as cell fate determination and people, concerning chiefs who have heldperfect: cell death (Abrahante et al., 2003, Brennecke dominion in the northern countries, and who et al., 2003, Chang et al., 2004, Chen et al., spoke the Danish tongue; and also concerning 2004, Johnston and Hobert, 2003, Lee et al., some of their family branches, according to 1993, ... what has been told me.Implications These results indicate that although Now it is said that ever since then wheneverare hedged, & miR-372&3 confer complete protection to the camel sees a place where ashes have been oncogene-induced senescence in a manner scattered, he wants to get revenge with hispresent tense similar to p53 inactivation, the cellular enemy the rat and stomps and rolls in the ashes+ that: response to DNA damage remains intact. hoping to get the rat.Monday, April 2, 2012
  116. 116. Anecdotal excursion into mythological text:Facts in the Endogenous small RNAs (miRNAs) I sing of golden-throned Hera whom Rheaeternal regulate gene expression by mechanisms bare. Queen of the immortals is she, surpassing conserved across metazoans. all in beauty: she is the sister and the wife ofpresent: 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 tosimple past: time investigating a juvenile in the first and gladsome song, and made them merry, and second sessions in experiments conducted in waited till evening should come; and as they the NAC and the striatum: T1 values were made merry dark evening came upon them. 122 ± 6 s and 114 ± 5 s.Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped withembedded the RASV12-ERTAM chimera gene, which sharp bronze, heavy and huge and strong, is only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-offacts: Vita et al, 2005). warriors, with whom she is wroth, she, the daughter of the mighty sire.Attribution in miRNAs have emerged as important In this book I have had old stories writtenthe present regulators of development and control down, as I have heard them told by intelligent processes such as cell fate determination and people, concerning chiefs who have heldperfect: cell death (Abrahante et al., 2003, Brennecke dominion in the northern countries, and who et al., 2003, Chang et al., 2004, Chen et al., spoke the Danish tongue; and also concerning 2004, Johnston and Hobert, 2003, Lee et al., some of their family branches, according to 1993, ... what has been told me.Implications These results indicate that although Now it is said that ever since then wheneverare hedged, & miR-372&3 confer complete protection to the camel sees a place where ashes have been oncogene-induced senescence in a manner scattered, he wants to get revenge with hispresent tense similar to p53 inactivation, the cellular enemy the rat and stomps and rolls in the ashes+ that: response to DNA damage remains intact. hoping to get the rat.Monday, April 2, 2012
  117. 117. Anecdotal excursion into mythological text:Facts in the Endogenous small RNAs (miRNAs) I sing of golden-throned Hera whom Rheaeternal regulate gene expression by mechanisms bare. Queen of the immortals is she, surpassing conserved across metazoans. all in beauty: she is the sister and the wife ofpresent: 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 tosimple past: time investigating a juvenile in the first and gladsome song, and made them merry, and second sessions in experiments conducted in waited till evening should come; and as they the NAC and the striatum: T1 values were made merry dark evening came upon them. 122 ± 6 s and 114 ± 5 s.Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped withembedded the RASV12-ERTAM chimera gene, which sharp bronze, heavy and huge and strong, is only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-offacts: Vita et al, 2005). warriors, with whom she is wroth, she, the daughter of the mighty sire.Attribution in miRNAs have emerged as important In this book I have had old stories writtenthe present regulators of development and control down, as I have heard them told by intelligent processes such as cell fate determination and people, concerning chiefs who have heldperfect: cell death (Abrahante et al., 2003, Brennecke dominion in the northern countries, and who et al., 2003, Chang et al., 2004, Chen et al., spoke the Danish tongue; and also concerning 2004, Johnston and Hobert, 2003, Lee et al., some of their family branches, according to 1993, ... what has been told me.Implications These results indicate that although Now it is said that ever since then wheneverare hedged, & miR-372&3 confer complete protection to the camel sees a place where ashes have been oncogene-induced senescence in a manner scattered, he wants to get revenge with hispresent tense similar to p53 inactivation, the cellular enemy the rat and stomps and rolls in the ashes+ that: response to DNA damage remains intact. hoping to get the rat.Monday, April 2, 2012
  118. 118. Anecdotal excursion into mythological text:Facts in the Endogenous small RNAs (miRNAs) I sing of golden-throned Hera whom Rheaeternal regulate gene expression by mechanisms bare. Queen of the immortals is she, surpassing conserved across metazoans. all in beauty: she is the sister and the wife ofpresent: 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 tosimple past: time investigating a juvenile in the first and gladsome song, and made them merry, and second sessions in experiments conducted in waited till evening should come; and as they the NAC and the striatum: T1 values were made merry dark evening came upon them. 122 ± 6 s and 114 ± 5 s.Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped withembedded the RASV12-ERTAM chimera gene, which sharp bronze, heavy and huge and strong, is only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-offacts: Vita et al, 2005). warriors, with whom she is wroth, she, the daughter of the mighty sire.Attribution in miRNAs have emerged as important In this book I have had old stories writtenthe present regulators of development and control down, as I have heard them told by intelligent processes such as cell fate determination and people, concerning chiefs who have heldperfect: cell death (Abrahante et al., 2003, Brennecke dominion in the northern countries, and who et al., 2003, Chang et al., 2004, Chen et al., spoke the Danish tongue; and also concerning 2004, Johnston and Hobert, 2003, Lee et al., some of their family branches, according to 1993, ... what has been told me.Implications These results indicate that although Now it is said that ever since then wheneverare hedged, & miR-372&3 confer complete protection to the camel sees a place where ashes have been oncogene-induced senescence in a manner scattered, he wants to get revenge with hispresent tense similar to p53 inactivation, the cellular enemy the rat and stomps and rolls in the ashes+ that: response to DNA damage remains intact. hoping to get the rat.Monday, April 2, 2012
  119. 119. Anecdotal excursion into mythological text:Facts in the Endogenous small RNAs (miRNAs) I sing of golden-throned Hera whom Rheaeternal regulate gene expression by mechanisms bare. Queen of the immortals is she, surpassing conserved across metazoans. all in beauty: she is the sister and the wife ofpresent: 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 tosimple past: time investigating a juvenile in the first and gladsome song, and made them merry, and second sessions in experiments conducted in waited till evening should come; and as they the NAC and the striatum: T1 values were made merry dark evening came upon them. 122 ± 6 s and 114 ± 5 s.Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped withembedded the RASV12-ERTAM chimera gene, which sharp bronze, heavy and huge and strong, is only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-offacts: Vita et al, 2005). warriors, with whom she is wroth, she, the daughter of the mighty sire.Attribution in miRNAs have emerged as important In this book I have had old stories writtenthe present regulators of development and control down, as I have heard them told by intelligent processes such as cell fate determination and people, concerning chiefs who have heldperfect: cell death (Abrahante et al., 2003, Brennecke dominion in the northern countries, and who et al., 2003, Chang et al., 2004, Chen et al., spoke the Danish tongue; and also concerning 2004, Johnston and Hobert, 2003, Lee et al., some of their family branches, according to 1993, ... what has been told me.Implications These results indicate that although Now it is said that ever since then wheneverare hedged, & miR-372&3 confer complete protection to the camel sees a place where ashes have been oncogene-induced senescence in a manner scattered, he wants to get revenge with hispresent tense similar to p53 inactivation, the cellular enemy the rat and stomps and rolls in the ashes+ that: response to DNA damage remains intact. hoping to get the rat.Monday, April 2, 2012
  120. 120. Realms and planes: Patterns and Blends Concepts ‘Present Argumenta tion: present Other/ Future Past Discour Work Present se Future Present Experiment PastMonday, April 2, 2012
  121. 121. Realms and planes: Patterns and Blends Concepts ‘Present Argumenta tion: present Other/ Future Past Discour Work Present se Future Present Experiment PastMonday, April 2, 2012

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