Stories that persuade with data

  • 2,586 views
Uploaded on

Talk on September 13, at Biocreative III in Bethesda, MD

Talk on September 13, at Biocreative III in Bethesda, MD

More in: Technology
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Be the first to comment
No Downloads

Views

Total Views
2,586
On Slideshare
0
From Embeds
0
Number of Embeds
1

Actions

Shares
Downloads
25
Comments
0
Likes
4

Embeds 0

No embeds

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
    No notes for slide

Transcript

  • 1. What is inside our full-text articles, and how do we improve access to it? Or: Stories, that persuade with data. Biocreative III Publishers Panel September 13, 2010 Anita de Waard, a.dewaard@elsevier.com Disruptive Technologies Director, Elsevier Labs
  • 2. Model of a paper: “Scientific articles are stories... 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 2 overexpress dAtx-1 show disorganized ommatidia and loss of she ate it all up.   Data interommatidial bristles (Figure 1F),
  • 3. Model of a paper: “Scientific articles are stories... 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 2 overexpress dAtx-1 show disorganized ommatidia and loss of she ate it all up.   Data interommatidial bristles (Figure 1F),
  • 4. “...that persuade (editors/authors/readers!)...” 3
  • 5. “...that persuade (editors/authors/readers!)...” 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 3 pathos, and often included a summing up. implications.
  • 6. “...that persuade (editors/authors/readers!)...” 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 3 pathos, and often included a summing up. implications.
  • 7. “... with data.” 4
  • 8. “... with data.” 4
  • 9. “... with data.” 4
  • 10. So how do we improve access to these? 5
  • 11. So how do we improve access to these? 1.1. Better access to ‘story’ elements: 5
  • 12. So how do we improve access to these? 1.1. Better access to ‘story’ elements: • Learn from Fairy Tale annotation/Proppian Markup? 5
  • 13. So how do we improve access to these? 1.1. Better access to ‘story’ elements: • Learn from Fairy Tale annotation/Proppian Markup? 5
  • 14. So how do we improve access to these? 1.1. Better access to ‘story’ elements: • Learn from Fairy Tale annotation/Proppian Markup? 5
  • 15. So how do we improve access to these? 1.1. Better access to ‘story’ elements: • Learn from Fairy Tale annotation/Proppian Markup? • W3C HCLS SiG Scientific discourse structure: 5
  • 16. So how do we improve access to these? 1.1. Better access to ‘story’ elements: • Learn from Fairy Tale annotation/Proppian Markup? • W3C HCLS SiG Scientific discourse structure: 5
  • 17. 1.2. Element access through Linked Data:
  • 18. 1.2. Element access through Linked Data: <ce:section id=#123>
  • 19. 1.2. Element access through Linked Data: this says <ce:section id=#123> mice like cheese
  • 20. 1.2. Element access through Linked Data: said @anita on September 8, 2010 this says <ce:section id=#123> mice like cheese
  • 21. 1.2. Element access through Linked Data: but we all know she was wrong then said @anita on September 8, 2010 this says <ce:section id=#123> mice like cheese
  • 22. 1.2. Element access through Linked Data: 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
  • 23. 1.2. Element access through Linked Data: 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
  • 24. 2.1. Improve access to persuasive elements: Identify key rhetorical elements in scientific text: 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. 7
  • 25. 2.1. Improve access to persuasive elements: Identify key rhetorical elements in scientific text: 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. 7
  • 26. 2.1. Improve access to persuasive elements: Identify key rhetorical elements in scientific text: 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. 7
  • 27. 2.1. Improve access to persuasive elements: Identify key rhetorical elements in scientific text: 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. 7
  • 28. 2.1. Improve access to persuasive elements: Identify key rhetorical elements in scientific text: 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. 7
  • 29. 2.1. Improve access to persuasive elements: Identify key rhetorical elements in scientific text: 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. 7
  • 30. 2.1. Improve access to persuasive elements: Identify key rhetorical elements in scientific text: 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. 7
  • 31. 2.1. Improve access to persuasive elements: Identify key rhetorical elements in scientific text: 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. 7
  • 32. 2.1. Improve access to persuasive elements: Identify key rhetorical elements in scientific text: 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. 7
  • 33. 2.1. Improve access to persuasive elements: Identify key rhetorical elements in scientific text: 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. 7
  • 34. 2.1. Improve access to persuasive elements: Identify key rhetorical elements in scientific text: 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. 7
  • 35. 2.2. Realms in experimental discourse
  • 36. 2.2. 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,
  • 37. 2.2. 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
  • 38. 2.2. 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),
  • 39. 2.2. 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),
  • 40. 2.2. 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),
  • 41. 2.2. 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),
  • 42. 2.2. 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
  • 43. 2.2. 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
  • 44. 2.3. Hypotheses, Evidence and Relationships: 9
  • 45. 2.3. Hypotheses, Evidence and Relationships: 9
  • 46. 2.3. Hypotheses, Evidence and Relationships: 9
  • 47. 2.3. Hypotheses, Evidence and Relationships: 9
  • 48. 2.3. Hypotheses, Evidence and Relationships: 9
  • 49. 2.3. Hypotheses, Evidence and Relationships: Hypothesis 22: Intramembrenous Aβ dimer may be toxic. Derived from: POSTAT_CONTRIBUTION(This essay explores the possibility that a fraction of these Abeta peptides never leave the membrane lipid bilayer after they are generated, but instead exert their toxic effects by competing with and compromising the functions of intramembranous segments of membrane-bound proteins that serve many critical functions. 9
  • 50. 2.3. Hypotheses, Evidence and Relationships: 9
  • 51. 2.3. Hypotheses, Evidence and Relationships: • Collective of groups working on representing scientific text as – discourse elements – linked by rhetorical relationships – connected to data 9
  • 52. 2.3. Hypotheses, Evidence and Relationships: • Collective of groups working on representing scientific text as – discourse elements – linked by rhetorical relationships – connected to data • Current efforts: – W3C HCLS SiG: development of a Rhetorical Document Structure – Unification of ScholOnto, CiTO, SWAN, SALT relations 9
  • 53. 2.3. Hypotheses, Evidence and Relationships: • Collective of groups working on representing scientific text as – discourse elements – linked by rhetorical relationships – connected to data • Current efforts: – W3C HCLS SiG: development of a Rhetorical Document Structure – Unification of ScholOnto, CiTO, SWAN, SALT relations • Developing an Annotation Framework with Harvard/MGH: – Access to collection of full-text content on Alzheimer’s – Allow standoff annotation through Harvard’s Annotation Ontology – Run several hypothesis/event identification tools - access through U-Compare, UMIA, SciKnowMine – Allow layering of annotations – Test with users in Alzheimer community! 9
  • 54. 2.4. Three dimensions of annotation: measure
  • 55. 2.4. Three dimensions of annotation: measure
  • 56. 2.4. Three dimensions of annotation: Granularity collection document claim triple entity measure
  • 57. 2.4. Three dimensions of annotation: Granularity collection document claim triple entity measure Means manual semi-automated automated
  • 58. 2.4. Three dimensions of annotation: Granularity collection document claim triple entity Mome measure author/editor typesetter/production reader/curator/data m Means manual semi-automated automated
  • 59. 2.4. Three dimensions of annotation: Granularity collection document claim triple entity Mome measure author/editor typesetter/production reader/curator/data m Means manual Entity Markup semi-automated automated
  • 60. 2.4. Three dimensions of annotation: Granularity collection document claim triple Hypothesis markup entity Mome measure author/editor typesetter/production reader/curator/data m Means manual Entity Markup semi-automated automated
  • 61. 2.4. Three dimensions of annotation: Granularity collection document claim triple Hypothesis markup entity Mome measure author/editor typesetter/production reader/curator/data m Means manual Entity Markup semi-automated automated
  • 62. 3.1. Research data
  • 63. 3.1. Research data ... gets created...
  • 64. 3.1. Research data ... gets created... ... and destroyed!
  • 65. 3.2. Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
  • 66. 3.2. Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan 1. Research: Each item in the system has metadata metadata (including provenance) and relations to other data items metadata added to it. metadata metadata metadata
  • 67. 3.2. Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan 1. Research: Each item in the system has metadata metadata (including provenance) and relations to other data items metadata added to it. 2. Workflow: All data items created in the lab are added metadata to a (lab-owned) workflow system. metadata metadata
  • 68. 3.2. Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan 1. Research: Each item in the system has metadata metadata (including provenance) and relations to other data items metadata added to it. 2. Workflow: All data items created in the lab are added metadata to a (lab-owned) workflow system. 3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document. metadata metadata Rats were subjected to two grueling tests (click on fig 2 to see underlying data). These results suggest that the neurological pain pro-
  • 69. 3.2. Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan 1. Research: Each item in the system has metadata metadata (including provenance) and relations to other data items metadata added to it. 2. Workflow: All data items created in the lab are added metadata to a (lab-owned) workflow system. 3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document. metadata 4. Editing and review: Once the co-authors agree, the paper is ‘exposed’ to the editors, who in turn expose it to metadata reviewers. Reports are stored in the authoring/editing system, the paper gets updated, until it is validated. Rats were subjected to two grueling tests (click on fig 2 to see underlying data). These results suggest that the neurological pain pro- Review Revise Edit
  • 70. 3.2. Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan 1. Research: Each item in the system has metadata metadata (including provenance) and relations to other data items metadata added to it. 2. Workflow: All data items created in the lab are added metadata to a (lab-owned) workflow system. 3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document. metadata 4. Editing and review: Once the co-authors agree, the paper is ‘exposed’ to the editors, who in turn expose it to metadata reviewers. Reports are stored in the authoring/editing system, the paper gets updated, until it is validated. 5. Publishing and distribution: When a paper is published, a collection of validated information is exposed to the world. It remains connected to its related Rats were subjected to two data item, and its heritage can be traced. grueling tests (click on fig 2 to see underlying data). These results suggest that the neurological pain pro- Review Revise Edit
  • 71. 3.2. Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan 1. Research: Each item in the system has metadata metadata (including provenance) and relations to other data items metadata added to it. 2. Workflow: All data items created in the lab are added metadata to a (lab-owned) workflow system. 3. Authoring: A paper is written in an authoring tool which can pull data with provenance from the workflow tool in the appropriate representation into the document. metadata 4. Editing and review: Once the co-authors agree, the paper is ‘exposed’ to the editors, who in turn expose it to metadata reviewers. Reports are stored in the authoring/editing system, the paper gets updated, until it is validated. 5. Publishing and distribution: When a paper is published, a collection of validated information is exposed to the world. It remains connected to its related Rats were subjected to two data item, and its heritage can be traced. grueling tests (click on fig 2 to see underlying 6. User applications: distributed applications run on this data). These results suggest that ‘exposed data’ universe. the neurological pain pro- Some other publisher Review Revise Edit
  • 72. 3.3. Small step: ScienceDirect app store
  • 73. 3.4. Social Change! Some next steps:
  • 74. 3.4. Social Change! Some next steps:
  • 75. 3.4. Social Change! Some next steps: • January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that
  • 76. 3.4. Social Change! Some next steps: • January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that • June 2011: ‘Executable Paper Challenge’ @ ICCS: ask computer scientists to submit ideas for ‘executable papers’ - embedded code or data
  • 77. 3.4. Social Change! Some next steps: • January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that • June 2011: ‘Executable Paper Challenge’ @ ICCS: ask computer scientists to submit ideas for ‘executable papers’ - embedded code or data • August 2011: Dagstuhl Workshop ‘Future of Research Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard):
  • 78. 3.4. Social Change! Some next steps: • January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that • June 2011: ‘Executable Paper Challenge’ @ ICCS: ask computer scientists to submit ideas for ‘executable papers’ - embedded code or data • August 2011: Dagstuhl Workshop ‘Future of Research Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard): –Involve key parties (scientists, publishers, funding bodies, libraries) to map out main bottlenecks
  • 79. 3.4. Social Change! Some next steps: • January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that • June 2011: ‘Executable Paper Challenge’ @ ICCS: ask computer scientists to submit ideas for ‘executable papers’ - embedded code or data • August 2011: Dagstuhl Workshop ‘Future of Research Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard): –Involve key parties (scientists, publishers, funding bodies, libraries) to map out main bottlenecks –Write white paper
  • 80. 3.4. Social Change! Some next steps: • January 2011: ‘Beyond the PDF’ workshop, Phil Bourne: linking data to papers; develop virtual community around that • June 2011: ‘Executable Paper Challenge’ @ ICCS: ask computer scientists to submit ideas for ‘executable papers’ - embedded code or data • August 2011: Dagstuhl Workshop ‘Future of Research Communications’ (Ed Hovy, Ivan Herman, Tim Clark, Anita de Waard): –Involve key parties (scientists, publishers, funding bodies, libraries) to map out main bottlenecks –Write white paper –Implement?!
  • 81. Questions? Interested in collaboration? a.dewaard@elsevier.com http://elsatglabs.com/labs/anita 15