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Stories, that persuade with data.   What’s inside scientific papers,   and should it be reengineered?  Anita de Waard, a.de...
Scientific papers are stories, that persuade with data.The Story of Goldilocks and              Story        Part        Pa...
Scientific papers are stories, that persuade with data.The Story of Goldilocks and              Story        Part        Pa...
Story analysis of scientific text:ORB vs. Medium-grained structure
Story analysis of scientific text:     ORB vs. Medium-grained structureSee work at http://www.w3.org/wiki/HCLSIG/SWANSIOC
Episode-level access through Linked Data standards:
Episode-level access through Linked Data standards:                                    said @anita                        ...
Episode-level access through Linked Data standards:                                        but we all know                ...
Episode-level access through Linked Data standards:the xml is fixed, but the structure is open!          allows for layers...
Satellite Format:Linked Data repository for all Elsevier content
Satellite Format:Linked Data repository for all Elsevier content                     Dublin Core and SKOS
Satellite Format:Linked Data repository for all Elsevier content                            Dublin Core and SKOS          ...
Scientific papers are stories,                that persuade with data.Both seminomas and the EC component ofnonseminomas sh...
Scientific papers are stories,                 that persuade with data.Both seminomas and the EC component of Both seminoma...
Scientific papers are stories,                 that persuade with data.Both seminomas and the EC component of Both seminoma...
Scientific papers are stories,                 that persuade with data.                                                    ...
Scientific papers are stories,                 that persuade with data.                                                    ...
Realms of persuasive experimental discourse:
Realms of persuasive experimental discourse:(1) Both seminomas             (2) b. the detection of                  (3) c....
Realms of persuasive experimental discourse:                               Concepts, models, ‘facts’(1) Both seminomas    ...
Realms of persuasive experimental discourse:                               Concepts, models, ‘facts’ ‘State’ present tense...
Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppre...
Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppre...
Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppre...
Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppre...
Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppre...
Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppre...
Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppre...
“[Y]ou can transform a fact into fiction or a fiction into fact    just by adding or subtracting references [and data]”     ...
“[Y]ou can transform a fact into fiction or a fiction into fact    just by adding or subtracting references [and data]”     ...
How is this rhetoric instantiated?Rhetorical            Utterance {Proposition}                                    S=     ...
Eventually: trace roots of a claim:how many independent data points is it based on?                                       ...
Eventually: trace roots of a claim:how many independent data points is it based on?          PHC   undergo Growth arrest  ...
Eventually: trace roots of a claim:how many independent data points is it based on?                   PHC       undergo Gr...
Eventually: trace roots of a claim:how many independent data points is it based on?                   PHC       undergo Gr...
Eventually: trace roots of a claim:how many independent data points is it based on?                   PHC       undergo Gr...
Eventually: trace roots of a claim:how many independent data points is it based on?                   PHC       undergo Gr...
Eventually: trace roots of a claim:how many independent data points is it based on?                   PHC       undergo Gr...
Eventually: trace roots of a claim:how many independent data points is it based on?                   PHC       undergo Gr...
Eventually: trace roots of a claim:how many independent data points is it based on?                   PHC        undergo G...
Scientific papers are stories,that persuade with data.
Scientific papers are stories,that persuade with data.
Scientific papers are stories,that persuade with data.
Sometimes the link to data is good:
And sometimes it’s not so good:
And sometimes it’s not so good:
And sometimes it’s not so good:
And sometimes it’s not so good:
Data-driven papers?   Work done with Ed Hovy, Phil Bourne,                      Gully Burns and Cartic Ramakrishnan
Data-driven papers?                                       Work done with Ed Hovy, Phil Bourne,                            ...
Data-driven papers?                                       Work done with Ed Hovy, Phil Bourne,                            ...
Data-driven papers?                                                   Work done with Ed Hovy, Phil Bourne,                ...
Data-driven papers?                                                   Work done with Ed Hovy, Phil Bourne,                ...
Data-driven papers?                                                   Work done with Ed Hovy, Phil Bourne,                ...
Data-driven papers?                                                   Work done with Ed Hovy, Phil Bourne,                ...
One step: encouraging submission   of structured workflows
Another step: ScienceDirect app store
Another step: ScienceDirect app store           - Eclipse SDK platform accessing all             ScienceDirect/Scopus cont...
A third step: Executable Paper ChallengeGoal: invite computer science community to help develop formats that:-   add execu...
A third step: Executable Paper ChallengeGoal: invite computer science community to help develop formats that:-   add execu...
In Summary:
In Summary:1. Stories:   -   ORB, Satellite: link to any part of content - bring it on!
In Summary:1. Stories:   -   ORB, Satellite: link to any part of content - bring it on!2. Persuasion:   -   Logical struct...
In Summary:1. Stories:   -   ORB, Satellite: link to any part of content - bring it on!2. Persuasion:   -   Logical struct...
In Summary:1. Stories:   -   ORB, Satellite: link to any part of content - bring it on!2. Persuasion:   -   Logical struct...
In Summary:1. Stories:    -   ORB, Satellite: link to any part of content - bring it on!2. Persuasion:    -   Logical stru...
Thank you!W3C group on Discourse Structure:http://www.w3.org/wiki/HCLSIG/SWANSIOCSciVerse: http://developer.sciverse.comPa...
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Reengineering the scientific research paper

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  • This Powerpoint, concerning the application of narrative science to scientific papers, is exciting and important. I have referred to this work in a blog post on the topic of sales and CRM ("customer relationship management") software. Sales is also very much about "narrative" and "story". And yet most, or even "all", sales and CRM software is terrible at enabled sales people to "maintain stories". As a high tech B2B sales person my job is to manage and progress between 20 and 40 stories. For a happy ending, or any ending. "Up or out". CRM is mainly transactional, which is sort of "after the fact". But stories are where the meaning and momentum of a potential commercial relationship are capture. Here's my blog post:
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Reengineering the scientific research paper

  1. 1. Stories, that persuade with data. What’s inside scientific papers, and should it be reengineered? Anita de Waard, a.dewaard@elsevier.comDisruptive Technologies Director, Elsevier Labs
  2. 2. Scientific papers are stories, that persuade with data.The Story of Goldilocks and Story Part Paper The AXH Domain of Ataxin-1 Mediatesthe Three Bears Neurodegeneration through Its Interaction with Gfi-1/ Senseless ProteinsOnce 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 forest. Location Experimental studied and compared in vivo effects and interactions to those of thePretty soon, she came upon a house. setup human proteinShe knocked and, when no one Goal Theme Research Gain insight into how Atx-1s function contributes to SCA1answered, goal pathogenesis. How these interactions might contribute to the disease process and how they might cause toxicity in only a subset of neurons inshe walked right in. Attempt Hypothesis SCA1 may play a role in the regulation of gene expression Atx-1 is not fully understood.At the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed inwere three bowls of porridge. FilesGoldilocks was hungry. Subgoal Subgoal test the function of the AXH domainShe tasted the porridge from the Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand andfirst bowl. 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 drivesexclaimed. expression in the differentiated R1-R6 photoreceptor cells (Mollereau et al., 2000 and OTousa et al., 1985), results in neurodegeneration in the eye, as does overexpression of hAtx-1[82Q]. Although at 2 days after eclosion, overexpression of either Atx-1 does not show obviousSo, she tasted the porridge from the Activity Data (data not shown), morphological changes in the photoreceptor cellssecond bowl.This porridge is too cold, she said Outcome Results both genotypes show many large holes and loss of cell integrity at 28 daysSo, she tasted the last bowl of Activity Data (Figures 1B-1D).porridge.Ahhh, this porridge is just right, she Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces eyesaid happily and abnormalities. The external structures of the eyes that overexpressshe ate it all up. Outcome Data dAtx-1 1F), disorganized ommatidia and loss of interommatidial bristles (Figure show
  3. 3. Scientific papers are stories, that persuade with data.The Story of Goldilocks and Story Part Paper The AXH Domain of Ataxin-1 Mediatesthe Three Bears Neurodegeneration through Its Interaction with Gfi-1/ Senseless ProteinsOnce 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 forest. Location Experimental studied and compared in vivo effects and interactions to those of thePretty soon, she came upon a house. setup human proteinShe knocked and, when no one Goal Theme Research Gain insight into how Atx-1s function contributes to SCA1answered, goal pathogenesis. How these interactions might contribute to the disease process and how they might cause toxicity in only a subset of neurons inshe walked right in. Attempt Hypothesis SCA1 may play a role in the regulation of gene expression Atx-1 is not fully understood.At the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed inwere three bowls of porridge. FilesGoldilocks was hungry. Subgoal Subgoal test the function of the AXH domainShe tasted the porridge from the Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand andfirst bowl. 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 drivesexclaimed. expression in the differentiated R1-R6 photoreceptor cells (Mollereau et al., 2000 and OTousa et al., 1985), results in neurodegeneration in the eye, as does overexpression of hAtx-1[82Q]. Although at 2 days after eclosion, overexpression of either Atx-1 does not show obviousSo, she tasted the porridge from the Activity Data (data not shown), morphological changes in the photoreceptor cellssecond bowl.This porridge is too cold, she said Outcome Results both genotypes show many large holes and loss of cell integrity at 28 daysSo, she tasted the last bowl of Activity Data (Figures 1B-1D).porridge.Ahhh, this porridge is just right, she Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver also induces eyesaid happily and abnormalities. The external structures of the eyes that overexpressshe ate it all up. Outcome Data dAtx-1 1F), disorganized ommatidia and loss of interommatidial bristles (Figure show
  4. 4. Story analysis of scientific text:ORB vs. Medium-grained structure
  5. 5. Story analysis of scientific text: ORB vs. Medium-grained structureSee work at http://www.w3.org/wiki/HCLSIG/SWANSIOC
  6. 6. Episode-level access through Linked Data standards:
  7. 7. Episode-level access through Linked Data standards: said @anita on April 5, 2011 this says<ce:section id=#123> mice like cheese
  8. 8. Episode-level access through Linked Data standards: but we all know she was deluded then said @anita on April 5, 2011 this says<ce:section id=#123> mice like cheese
  9. 9. Episode-level access through Linked Data standards:the xml is fixed, but the structure is open! allows for layers of annotation but we all know she was deluded then said @anita on April 5, 2011 this says <ce:section id=#123> mice like cheese
  10. 10. Satellite Format:Linked Data repository for all Elsevier content
  11. 11. Satellite Format:Linked Data repository for all Elsevier content Dublin Core and SKOS
  12. 12. Satellite Format:Linked Data repository for all Elsevier content Dublin Core and SKOS SWAN’s PAV (Provenance, Authoring and Versioning) ontology
  13. 13. Scientific papers are stories, that persuade with data.Both seminomas and the EC component ofnonseminomas share features with ES cells. Toexclude that the detection of miR-371-3 merelyreflects its expression pattern in ES cells, we testedby RPA miR-302a-d, another ES cells-specificmiRNA cluster (Suh et al, 2004). In many of themiR-371-3 expressing seminomas andnonseminomas, miR-302a-d was undetectable (FigsS7 and S8), suggesting that miR-371-3 expressionis a selective event during tumorigenesis.
  14. 14. Scientific papers are stories, that persuade with data.Both seminomas and the EC component of Both seminomas and the EC component ofnonseminomas share features with ES cells. nonseminomas share features with ES cells. Toexclude thatthat detection of miR-371-3 merely To exclude thereflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we testedby 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 them 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 mnonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomasS7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expressionis a selective event during tumorigenesis. (Figs S7 and S8), suggesting that miR-371-3 expression is a selective event during tumorigenesis.
  15. 15. Scientific papers are stories, that persuade with data.Both seminomas and the EC component of Both seminomas and the EC component of Factnonseminomas share features with ES cells. nonseminomas share features with ES cells. Toexclude thatthat detection of miR-371-3 merely To exclude the Goalreflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested Hypothesisby 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 them 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 Methodnonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomasS7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression Resultis a selective event during tumorigenesis. (Figs S7 and S8), suggesting that Reg-Implication miR-371-3 expression is a selective event during Implication tumorigenesis.
  16. 16. Scientific papers are stories, that persuade with data. ConceptualBoth seminomas and the EC component of Both seminomas and the EC component of knowledge Factnonseminomas share features with ES cells. nonseminomas share features with ES cells. Toexclude thatthat detection of miR-371-3 merely To exclude the Goalreflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested Hypothesisby 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 them 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 Methodnonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomasS7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression Resultis a selective event during tumorigenesis. (Figs S7 and S8), suggesting that Reg-Implication miR-371-3 expression is a selective event during Implication tumorigenesis.
  17. 17. Scientific papers are stories, that persuade with data. ConceptualBoth seminomas and the EC component of Both seminomas and the EC component of knowledge Factnonseminomas share features with ES cells. nonseminomas share features with ES cells. Toexclude thatthat detection of miR-371-3 merely To exclude the Goalreflects its expression pattern in ES cells,reflects its the detection of miR-371-3 merely we tested Hypothesisby 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 them 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 Experimentalnonseminomas, miR-302a-d was undetectable (Figs In many of the miR-371-3 expressing seminomas EvidenceS7 and S8), suggesting that miR-371-3undetectable and nonseminomas, miR-302a-d was expression Resultis a selective event during tumorigenesis. (Figs S7 and S8), suggesting that Reg-Implication miR-371-3 expression is a selective event during Implication tumorigenesis.
  18. 18. Realms of persuasive experimental discourse:
  19. 19. Realms of persuasive experimental discourse:(1) Both seminomas (2) b. the detection of (3) c. miR-371-3and the EC component miR-371-3 merely expression is aof nonseminomas share reflects its expression selective event duringfeatures 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),
  20. 20. Realms of persuasive experimental discourse: Concepts, models, ‘facts’(1) Both seminomas (2) b. the detection of (3) c. miR-371-3and the EC component miR-371-3 merely expression is aof nonseminomas share reflects its expression selective event duringfeatures 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
  21. 21. Realms of persuasive experimental discourse: Concepts, models, ‘facts’ ‘State’ present tense(1) Both seminomas (2) b. the detection of (3) c. miR-371-3and the EC component miR-371-3 merely expression is aof nonseminomas share reflects its expression selective event duringfeatures 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 ‘Narrative’ past tense
  22. 22. Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppress theexpression of LATS2, we...Therefore, these results point to LATS2 as a mediator of the miR-372 andmiR-373 effects on cell proliferation and tumorigenicity,
  23. 23. Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppress the Hypothesisexpression of LATS2, we...Therefore, these results point to LATS2 as a mediator of the miR-372 andmiR-373 effects on cell proliferation and tumorigenicity,
  24. 24. Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppress the Hypothesisexpression of LATS2, we...Therefore, these results point to LATS2 as a mediator of the miR-372 andmiR-373 effects on cell proliferation and tumorigenicity, Implication
  25. 25. Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppress the Hypothesisexpression of LATS2, we...Therefore, these results point to LATS2 as a mediator of the miR-372 andmiR-373 effects on cell proliferation and tumorigenicity, ImplicationRaver-Shapira et.al, JMolCell 2007... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes intesticular germ cell tumors by inhibition of LATS2 expression, which suggeststhat Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).
  26. 26. Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppress the Hypothesisexpression of LATS2, we...Therefore, these results point to LATS2 as a mediator of the miR-372 andmiR-373 effects on cell proliferation and tumorigenicity, ImplicationRaver-Shapira et.al, JMolCell 2007 Cited Implication... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes intesticular germ cell tumors by inhibition of LATS2 expression, which suggeststhat Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).
  27. 27. Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppress the Hypothesisexpression of LATS2, we...Therefore, these results point to LATS2 as a mediator of the miR-372 andmiR-373 effects on cell proliferation and tumorigenicity, ImplicationRaver-Shapira et.al, JMolCell 2007 Cited Implication... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes intesticular germ cell tumors by inhibition of LATS2 expression, which suggeststhat Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).Yabuta, JBioChem 2007:miR-372 and miR-373 target the Lats2 tumor suppressor (Voorhoeve et al., 2006)
  28. 28. Fact creation through citations:Voorhoeve et al, Cell, 2006:To investigate the possibility that miR-372 and miR-373 suppress the Hypothesisexpression of LATS2, we...Therefore, these results point to LATS2 as a mediator of the miR-372 andmiR-373 effects on cell proliferation and tumorigenicity, ImplicationRaver-Shapira et.al, JMolCell 2007 Cited Implication... two miRNAs, miRNA-372 and-373, function as potential novel oncogenes intesticular germ cell tumors by inhibition of LATS2 expression, which suggeststhat Lats2 is an important tumor suppressor (Voorhoeve et al., 2006).Yabuta, JBioChem 2007: FactmiR-372 and miR-373 target the Lats2 tumor suppressor (Voorhoeve et al., 2006)
  29. 29. “[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
  30. 30. “[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
  31. 31. How is this rhetoric instantiated?Rhetorical Utterance {Proposition} S= V=goal H, B C, EIndicate lack of {The role of untranslated exons in the CCR3 gene} NN 0knowledge has not been studied.Evaluate other Recently, CCR3 has been shown to {be N, D 3work upregulated on neutrophils by interferons in vitro [..]}Offer it is thought that {these transcription factors NN, R 2hypotheses affect transcription of the gene through interactions with the RNA transcription complex.}Interpret results these data suggested that {5 untranslated exon A, D 2 1 may have a regulatory function.}Assess validity Since {this was not the case with other lines,} {we A, D 1of suspect {it is integration-site specific}}interpretationsState While we expected {the transcript to be about 1 A, D 2, S+correspondence kb in size (Figure 4A),} {two bands ~4 and 5 kb wereto expectations apparent.}Comparison to It is important that {this data be viewed A,R/ 2, F+other work with {what is known about other myeloid- NN/ specific promoters,}} D
  32. 32. Eventually: trace roots of a claim:how many independent data points is it based on? 11
  33. 33. Eventually: trace roots of a claim:how many independent data points is it based on? PHC undergo Growth arrest 11
  34. 34. Eventually: trace roots of a claim:how many independent data points is it based on? PHC undergo Growth arrestPaper A: implication method fact goal fact results data 1 data 2 data 3 11
  35. 35. Eventually: trace roots of a claim:how many independent data points is it based on? PHC undergo Growth arrestPaper A: Paper B: implication implication method fact method fact goal fact goal fact results results data 1 data 4 data 2 data 3 data 5 data 6 11
  36. 36. Eventually: trace roots of a claim:how many independent data points is it based on? PHC undergo Growth arrestPaper A: Paper B: implication implication method fact method fact goal fact goal fact results results data 1 data 4 data 2 data 3 data 5 data 6 11
  37. 37. Eventually: trace roots of a claim:how many independent data points is it based on? PHC undergo Growth arrestPaper A: Paper B: implication implication method fact method fact goal fact goal fact results results data 1 data 4 data 2 data 3 data 5 data 6 11
  38. 38. Eventually: trace roots of a claim:how many independent data points is it based on? PHC undergo Growth arrestPaper A: Paper B: implication implication g nnin method fact rpi method de fact un goal fact goal fact results results data 1 data 4 data 2 data 3 data 5 data 6 11
  39. 39. Eventually: trace roots of a claim:how many independent data points is it based on? PHC undergo Growth arrestPaper A: Paper B: implication implication method fact method fact goal fact goal fact results results data 1 data 4 data 2 data 3 data 5 data 6 11
  40. 40. Eventually: trace roots of a claim:how many independent data points is it based on? PHC undergo Growth arrestPaper A: Paper B: implication implication method method link fact method fact goal fact goal fact results results data 1 data 4 data 2 data 3 data 5 data 6 11
  41. 41. Scientific papers are stories,that persuade with data.
  42. 42. Scientific papers are stories,that persuade with data.
  43. 43. Scientific papers are stories,that persuade with data.
  44. 44. Sometimes the link to data is good:
  45. 45. And sometimes it’s not so good:
  46. 46. And sometimes it’s not so good:
  47. 47. And sometimes it’s not so good:
  48. 48. And sometimes it’s not so good:
  49. 49. Data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
  50. 50. 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
  51. 51. 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 addedmetadata to a (lab-owned) workflow system. metadata metadata
  52. 52. 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 metadataRats were subjected to two gruelingtests(click on fig 2 to see underlyingdata). These results suggest that theneurological pain pro-
  53. 53. 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
  54. 54. 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 grueling data item, and its heritage can be traced. tests (click on fig 2 to see underlying data). These results suggest that the neurological pain pro-Review Revise Edit
  55. 55. 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 grueling data item, and its heritage can be traced. tests (click on fig 2 to see underlying 6. User applications: distributed applications run on this data). These results suggest that the ‘exposed data’ universe. neurological pain pro- Some other publisherReview Revise Edit
  56. 56. One step: encouraging submission of structured workflows
  57. 57. Another step: ScienceDirect app store
  58. 58. Another step: ScienceDirect app store - Eclipse SDK platform accessing all ScienceDirect/Scopus content - Build applications on top of content - Offer to users in marketplace
  59. 59. A third step: Executable Paper ChallengeGoal: invite computer science community to help develop formats that:- add executable files and reproducible data to computer science papers;- handle storage and validation of very large files- help validation of data and code, and decrease the reviewer’s workload
  60. 60. A third step: Executable Paper ChallengeGoal: invite computer science community to help develop formats that:- add executable files and reproducible data to computer science papers;- handle storage and validation of very large files- help validation of data and code, and decrease the reviewer’s workload
  61. 61. In Summary:
  62. 62. In Summary:1. Stories: - ORB, Satellite: link to any part of content - bring it on!
  63. 63. In Summary:1. Stories: - ORB, Satellite: link to any part of content - bring it on!2. Persuasion: - Logical structure for biological propositions; trace a claim through successive citations
  64. 64. In Summary:1. Stories: - ORB, Satellite: link to any part of content - bring it on!2. Persuasion: - Logical structure for biological propositions; trace a claim through successive citations3. Data: - Better data linking, better structuring of methods.
  65. 65. In Summary:1. Stories: - ORB, Satellite: link to any part of content - bring it on!2. Persuasion: - Logical structure for biological propositions; trace a claim through successive citations3. Data: - Better data linking, better structuring of methods.In conclusion: is the research paper going away?
  66. 66. In Summary:1. Stories: - ORB, Satellite: link to any part of content - bring it on!2. Persuasion: - Logical structure for biological propositions; trace a claim through successive citations3. Data: - Better data linking, better structuring of methods.In conclusion: is the research paper going away?I don’t think so! But it will be: - Structured better: authors will need to justify claims directly - Connected better: more traceable, better links to data and workflow components, and to other work
  67. 67. Thank you!W3C group on Discourse Structure:http://www.w3.org/wiki/HCLSIG/SWANSIOCSciVerse: http://developer.sciverse.comPangea project: http://bit.ly/98haOwParsing rhetoric: http://elsatglabs.com/labs/anita/Fact creation demo: http://elsatglabs.com/labs/anita/demos/LATSDemo102007/Methods Navigator: http://www.methodsnavigator.comSciVerse APIs: http://developer.sciverse.comExecutable Paper Challenge: http://www.executablepapers.comOr mail me at:Anita de Waard, a.dewaard@elsevier.com

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