Overview of scientific discourse annotatoin

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Presentation held at second Amicus workshop, http://amicus.uvt.nl/amicus_ws2011.htm: "Storytelling in Fairytales and Science:
Narrative structure models of scientific communication and folktales"

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Overview of scientific discourse annotatoin

  1. 1. A  brief  introduc.on  to   current  efforts  in scien.fic  discourse  annota.on   Anita  de  Waard Disrup/ve  Technology  Director,  Elsevier  Labs -­‐  also  on  behalf  of  HCLS/UU/D2S... hEp://elsatglabs.com/labs/anita  Thursday, October 20, 2011
  2. 2. One  way  of  subdividing  the  field  of Scien/fic  Discourse  Annota/on: 2Thursday, October 20, 2011
  3. 3. One  way  of  subdividing  the  field  of Scien/fic  Discourse  Annota/on: Five  levels  of  markup:   2Thursday, October 20, 2011
  4. 4. One  way  of  subdividing  the  field  of Scien/fic  Discourse  Annota/on: Five  levels  of  markup:   1.Sec/on:  “Discussion”,  ~  several  paragraphs  (+HCLS) 2Thursday, October 20, 2011
  5. 5. One  way  of  subdividing  the  field  of Scien/fic  Discourse  Annota/on: Five  levels  of  markup:   1.Sec/on:  “Discussion”,  ~  several  paragraphs  (+HCLS) 2.Module:  “Research  Ques/on”,  ~  paragraph 2Thursday, October 20, 2011
  6. 6. One  way  of  subdividing  the  field  of Scien/fic  Discourse  Annota/on: Five  levels  of  markup:   1.Sec/on:  “Discussion”,  ~  several  paragraphs  (+HCLS) 2.Module:  “Research  Ques/on”,  ~  paragraph 3.Statement:  “Hypothesis”,  ~  sentence/clause  (+UU) 2Thursday, October 20, 2011
  7. 7. One  way  of  subdividing  the  field  of Scien/fic  Discourse  Annota/on: Five  levels  of  markup:   1.Sec/on:  “Discussion”,  ~  several  paragraphs  (+HCLS) 2.Module:  “Research  Ques/on”,  ~  paragraph 3.Statement:  “Hypothesis”,  ~  sentence/clause  (+UU) 4.Rela/on:  “Supports”,  ~  hyperlink (En/ty:  “Gene  Name”,  ~  NP) 2Thursday, October 20, 2011
  8. 8. One  way  of  subdividing  the  field  of Scien/fic  Discourse  Annota/on: Five  levels  of  markup:   1.Sec/on:  “Discussion”,  ~  several  paragraphs  (+HCLS) 2.Module:  “Research  Ques/on”,  ~  paragraph 3.Statement:  “Hypothesis”,  ~  sentence/clause  (+UU) 4.Rela/on:  “Supports”,  ~  hyperlink (En/ty:  “Gene  Name”,  ~  NP) 5.Special  case  of  3&4:  Claim/Evidence  network  (+D2S) 2Thursday, October 20, 2011
  9. 9. One  way  of  subdividing  the  field  of Scien/fic  Discourse  Annota/on: Five  levels  of  markup:   1.Sec/on:  “Discussion”,  ~  several  paragraphs  (+HCLS) 2.Module:  “Research  Ques/on”,  ~  paragraph 3.Statement:  “Hypothesis”,  ~  sentence/clause  (+UU) 4.Rela/on:  “Supports”,  ~  hyperlink (En/ty:  “Gene  Name”,  ~  NP) 5.Special  case  of  3&4:  Claim/Evidence  network  (+D2S) For  each  level:   2Thursday, October 20, 2011
  10. 10. One  way  of  subdividing  the  field  of Scien/fic  Discourse  Annota/on: Five  levels  of  markup:   1.Sec/on:  “Discussion”,  ~  several  paragraphs  (+HCLS) 2.Module:  “Research  Ques/on”,  ~  paragraph 3.Statement:  “Hypothesis”,  ~  sentence/clause  (+UU) 4.Rela/on:  “Supports”,  ~  hyperlink (En/ty:  “Gene  Name”,  ~  NP) 5.Special  case  of  3&4:  Claim/Evidence  network  (+D2S) For  each  level:   a) Why?  Use  cases   2Thursday, October 20, 2011
  11. 11. One  way  of  subdividing  the  field  of Scien/fic  Discourse  Annota/on: Five  levels  of  markup:   1.Sec/on:  “Discussion”,  ~  several  paragraphs  (+HCLS) 2.Module:  “Research  Ques/on”,  ~  paragraph 3.Statement:  “Hypothesis”,  ~  sentence/clause  (+UU) 4.Rela/on:  “Supports”,  ~  hyperlink (En/ty:  “Gene  Name”,  ~  NP) 5.Special  case  of  3&4:  Claim/Evidence  network  (+D2S) For  each  level:   a) Why?  Use  cases   b) What,  by  whom?  Concepts,  ontology,  authors? 2Thursday, October 20, 2011
  12. 12. One  way  of  subdividing  the  field  of Scien/fic  Discourse  Annota/on: Five  levels  of  markup:   1.Sec/on:  “Discussion”,  ~  several  paragraphs  (+HCLS) 2.Module:  “Research  Ques/on”,  ~  paragraph 3.Statement:  “Hypothesis”,  ~  sentence/clause  (+UU) 4.Rela/on:  “Supports”,  ~  hyperlink (En/ty:  “Gene  Name”,  ~  NP) 5.Special  case  of  3&4:  Claim/Evidence  network  (+D2S) For  each  level:   a) Why?  Use  cases   b) What,  by  whom?  Concepts,  ontology,  authors? c) How?  Manual,  automated?   2Thursday, October 20, 2011
  13. 13. 1.  Sec/on-­‐level  markup 3Thursday, October 20, 2011
  14. 14. 1.  Sec/on-­‐level  markup INTRODUCTION 3Thursday, October 20, 2011
  15. 15. 1.  Sec/on-­‐level  markupa.Why  mark  up  sec/ons? -­‐ Search:  e.g.  search  for  en//es   in  Methods -­‐ Visualisa/on:  e.g.  structured   browse  at  sec/on  level INTRODUCTION 3Thursday, October 20, 2011
  16. 16. 1.  Sec/on-­‐level  markupa.Why  mark  up  sec/ons? -­‐ Search:  e.g.  search  for  en//es   in  Methods -­‐ Visualisa/on:  e.g.  structured   browse  at  sec/on  levelb.What,  by  whom? -­‐ Background/Contribu/on/ Discussion  model  for  CS INTRODUCTION -­‐ HCLS:  Ontology  of  Rhetorical   Blocks  (ORB)=  IMRaD  in  OWL 3Thursday, October 20, 2011
  17. 17. 1.  Sec/on-­‐level  markupa.Why  mark  up  sec/ons? -­‐ Search:  e.g.  search  for  en//es   Annotation in  Methods -­‐ Visualisa/on:  e.g.  structured   browse  at  sec/on  levelb.What,  by  whom? -­‐ Background/Contribu/on/ Discussion  model  for  CS INTRODUCTION -­‐ HCLS:  Ontology  of  Rhetorical   Blocks  (ORB)=  IMRaD  in  OWL 3Thursday, October 20, 2011
  18. 18. 1.  Sec/on-­‐level  markupa.Why  mark  up  sec/ons? -­‐ Search:  e.g.  search  for  en//es   Annotation in  Methods -­‐ Visualisa/on:  e.g.  structured   browse  at  sec/on  levelb.What,  by  whom? -­‐ Background/Contribu/on/ Discussion  model  for  CS INTRODUCTION -­‐ HCLS:  Ontology  of  Rhetorical   Blocks  (ORB)=  IMRaD  in  OWLc. Automate?   -­‐ Yes  -­‐[Hovy/Ramakrishnan] 3Thursday, October 20, 2011
  19. 19. HCLS  SciDis:  develop  standards  for  this  markup 4Thursday, October 20, 2011
  20. 20. 2.a.  Module-­‐level  markup:  why? -­‐ BeEer  search:  e.g.  query  inside  ‘Research  ques/on’ -­‐ Ini/al  idea:  content  reuse,  e.g. -­‐ Write  Methods  sec/ons  once,  import/link  many -­‐ Different  way  of  crea/ng  a  collec/on  of  scholarly   content:  not  standalone  narra/ve,  but  connected   set  of  modules   5Thursday, October 20, 2011
  21. 21. 2.b.  Module-­‐level  markup:  What,  by  whom?   6Thursday, October 20, 2011
  22. 22. 2.b.  Module-­‐level  markup:  What,  by  whom?   -­‐ Kircz,  ’98:  “a  much  more  radical   approach  would  be  to  [break]  apart  the   linear  text  into  independent  modules,   each  with  its  own  unique  cogni/ve   character.” 6Thursday, October 20, 2011
  23. 23. 2.b.  Module-­‐level  markup:  What,  by  whom?   -­‐ Kircz,  ’98:  “a  much  more  radical   approach  would  be  to  [break]  apart  the   linear  text  into  independent  modules,   each  with  its  own  unique  cogni/ve   character.” 6Thursday, October 20, 2011
  24. 24. 2.b.  Module-­‐level  markup:  What,  by  whom?   -­‐ Kircz,  ’98:  “a  much  more  radical   approach  would  be  to  [break]  apart  the   linear  text  into  independent  modules,   each  with  its  own  unique  cogni/ve   character.” -­‐ Harmsze,  ‘00:  modular  model  for   physics  papers 6Thursday, October 20, 2011
  25. 25. 2.b.  Module-­‐level  markup:  What,  by  whom?   -­‐ Kircz,  ’98:  “a  much  more  radical   approach  would  be  to  [break]  apart  the   linear  text  into  independent  modules,   each  with  its  own  unique  cogni/ve   character.” -­‐ Harmsze,  ‘00:  modular  model  for   physics  papers 6Thursday, October 20, 2011
  26. 26. 2.b.  Module-­‐level  markup:  What,  by  whom?   -­‐ Kircz,  ’98:  “a  much  more  radical   approach  would  be  to  [break]  apart  the   linear  text  into  independent  modules,   each  with  its  own  unique  cogni/ve   character.” -­‐ Harmsze,  ‘00:  modular  model  for   physics  papers -­‐ LiquidPub,  2010:  Structured  Knowledge   Objects   6Thursday, October 20, 2011
  27. 27. 2.b.  Module-­‐level  markup:  What,  by  whom?   -­‐ Kircz,  ’98:  “a  much  more  radical   approach  would  be  to  [break]  apart  the   linear  text  into  independent  modules,   each  with  its  own  unique  cogni/ve   character.” -­‐ Harmsze,  ‘00:  modular  model  for   physics  papers -­‐ LiquidPub,  2010:  Structured  Knowledge   Objects   6Thursday, October 20, 2011
  28. 28. 2.b.  Module-­‐level  markup:  What,  by  whom?   -­‐ Kircz,  ’98:  “a  much  more  radical   approach  would  be  to  [break]  apart  the   linear  text  into  independent  modules,   each  with  its  own  unique  cogni/ve   character.” -­‐ Harmsze,  ‘00:  modular  model  for   physics  papers -­‐ LiquidPub,  2010:  Structured  Knowledge   Objects   -­‐ HCLS:  Medium-­‐grained  structure:   core  narra/ve  components 6Thursday, October 20, 2011
  29. 29. 2.b.  Module-­‐level  markup:  What,  by  whom?   -­‐ Kircz,  ’98:  “a  much  more  radical   approach  would  be  to  [break]  apart  the   linear  text  into  independent  modules,   each  with  its  own  unique  cogni/ve   character.” -­‐ Harmsze,  ‘00:  modular  model  for   physics  papers -­‐ LiquidPub,  2010:  Structured  Knowledge   Objects   -­‐ HCLS:  Medium-­‐grained  structure:   core  narra/ve  components 6Thursday, October 20, 2011
  30. 30. Story  grammar  model  for  scienceThe Story of Goldilocks and Story Grammar 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 ofPretty soon, she came upon a setup the human proteinhouse.She 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 ashe walked right in. subset of neurons in SCA1 is not fully understood. Atx-1 may play a role in the regulation of gene expression Attempt HypothesisAt the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes Whenwere three bowls of porridge. Overexpressed in 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 systemfirst bowl. (Brand and Perrimon, 1993) and compared its effects to those ofThis porridge is too hot! she Outcome Results hAtx-1. Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, whichexclaimed. drives 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 eitherSo, she tasted the porridge from Activity Data (data not shown), Atx-1 does not show obvious morphological changes in thethe second bowl. photoreceptor cellsThis 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, Outcome Results Overexpression of dAtx-1 using the GMR-GAL4 driver alsoshe said happily and induces eye abnormalities. The external structures of the eyes 7 that overexpress dAtx-1 show disorganized ommatidia and lossshe ate it all up.   Data (Figure 1F), of interommatidial bristlesThursday, October 20, 2011
  31. 31. 2.c.  Module-­‐level  markup:  how? 8Thursday, October 20, 2011
  32. 32. 2.c.  Module-­‐level  markup:  how? -­‐ Automated  recogni/on:  very  difficult: 8Thursday, October 20, 2011
  33. 33. 2.c.  Module-­‐level  markup:  how? -­‐ Automated  recogni/on:  very  difficult: -­‐ How  do  you  know  where  the  boundaries  are?   8Thursday, October 20, 2011
  34. 34. 2.c.  Module-­‐level  markup:  how? -­‐ Automated  recogni/on:  very  difficult: -­‐ How  do  you  know  where  the  boundaries  are?   -­‐ Even  difficult  for  author  to  iden/fy!   8Thursday, October 20, 2011
  35. 35. 2.c.  Module-­‐level  markup:  how? -­‐ Automated  recogni/on:  very  difficult: -­‐ How  do  you  know  where  the  boundaries  are?   -­‐ Even  difficult  for  author  to  iden/fy!   -­‐ Author  creates:  templates. 8Thursday, October 20, 2011
  36. 36. 2.c.  Module-­‐level  markup:  how? -­‐ Automated  recogni/on:  very  difficult: -­‐ How  do  you  know  where  the  boundaries  are?   -­‐ Even  difficult  for  author  to  iden/fy!   -­‐ Author  creates:  templates. -­‐ XPharm,  2001:  modular  text  book  in  pharmacology: 8Thursday, October 20, 2011
  37. 37. 2.c.  Module-­‐level  markup:  how? -­‐ Automated  recogni/on:  very  difficult: -­‐ How  do  you  know  where  the  boundaries  are?   -­‐ Even  difficult  for  author  to  iden/fy!   -­‐ Author  creates:  templates. -­‐ XPharm,  2001:  modular  text  book  in  pharmacology: 8Thursday, October 20, 2011
  38. 38. 2.c.  Module-­‐level  markup:  how? -­‐ Automated  recogni/on:  very  difficult: -­‐ How  do  you  know  where  the  boundaries  are?   -­‐ Even  difficult  for  author  to  iden/fy!   -­‐ Author  creates:  templates. -­‐ XPharm,  2001:  modular  text  book  in  pharmacology: -­‐ Only  works  if  you   pay  authors! 8Thursday, October 20, 2011
  39. 39. 2.c.  Module-­‐level  markup:  how? -­‐ Automated  recogni/on:  very  difficult: -­‐ How  do  you  know  where  the  boundaries  are?   -­‐ Even  difficult  for  author  to  iden/fy!   -­‐ Author  creates:  templates. -­‐ XPharm,  2001:  modular  text  book  in  pharmacology: -­‐ Only  works  if  you   pay  authors! -­‐ Mo/f  detec/on  work might  offer  help?   8Thursday, October 20, 2011
  40. 40. 3.  Statement-­‐level  markup 9Thursday, October 20, 2011
  41. 41. 3.  Statement-­‐level  markup a.Why? -­‐ Automated  summarisa/on? -­‐ Towards  claim-­‐evidence  networks 9Thursday, October 20, 2011
  42. 42. 3.  Statement-­‐level  markup a.Why? -­‐ Automated  summarisa/on? -­‐ Towards  claim-­‐evidence  networks b.How,  by  whom?   -­‐ Comparison  of  three  groups:   1.Liakata  et  al.:  CoreSC 2.Ananiadou  et  al.:  Metaknowledge  annota/on 3.De  Waard/Pander  Maat:  Discourse  Segment  Types -­‐ Annotated  three  texts:  compare  schemes,  levels,   annota/on  overlap 9Thursday, October 20, 2011
  43. 43. 3.1  Liakata  et  al.:  Core-­‐Scien/fic  Concepts   (CoreSC)  Annota/on  Scheme sThursday, October 20, 2011
  44. 44. 3.1  Liakata  et  al.:  Core-­‐Scien/fic  Concepts   (CoreSC)  Annota/on  Scheme Three-­‐layer,  ontology-­‐mo/vated  annota/on  scheme  for  sentence   annota/on,  which  views  a  paper  as  the  humanly  readable   representa0on  of  a  scien0fic  inves0ga0on:  [45-­‐page  guideline:   Liakata  &  Soldatova  2008]   -­‐ 1st  layer:  Core  Scien4fic  Concepts  (CoreSCs):   Hypothesis,  Mo/va/on,  Goal,  Object,  Background,  Method,   Experiment,  Model,  Observa/on,  Result,  Conclusion   -­‐ 2nd  layer:  Proper4es  of  CoreSCs.   s Novelty  (New/Old)  and  Advantage  (advantage/disadvantage) -­‐ 3rd  layer:  Concept  Iden4fiers:   linking  sentences  together  which  refer  to  the  same  instance  of   a  CoreSCThursday, October 20, 2011
  45. 45. 3.1  CoreSC  Annota/on  tool:Thursday, October 20, 2011
  46. 46. 3.1  CoreSC  Annota/on  tool:• Automated  annota/on  with  CoreSC  system  well  underway!Thursday, October 20, 2011
  47. 47. 3.2.  Ananiadou  et  al:  Metaknowledge  annota/on: Knowledge  Type Certainty  Level •  Inves4ga4on •L3 •  Observa4on •L2 •  Analysis •L1 •  General Par4cipants Bio-­‐Event Class  /  Type •  Theme(s) (Centred  on  an  Event   (Grounded  to  an  event   •  Actor(s) Trigger) ontology) Source Manner Polarity •  High •  Other •  Nega4ve •  Low •  Current •  Posi4ve •  NeutralThursday, October 20, 2011
  48. 48. 3.2  Example  of  Metaknowledge  annota/on: S3 = These results suggest that Y has no effect on expression of X Knowledge Certainty Lexical   Event Manner Source Type Level Polarity E1 General L3 Posi4ve Neutral Current E2 Analysis L2 Nega4ve Neutral CurrentThursday, October 20, 2011
  49. 49. 3.2  Example  of  Metaknowledge  annota/on: S3 = These results suggest that Y has no effect on expression of X Knowledge Certainty Lexical   Event Manner Source Type Level Polarity E1 General L3 Posi4ve Neutral Current E2 Analysis L2 Nega4ve Neutral CurrentThursday, October 20, 2011
  50. 50. 3.2  Example  of  Metaknowledge  annota/on: S3 = These results suggest that Y has no effect on expression of X Knowledge Certainty Lexical   Event Manner Source Type Level Polarity E1 General L3 Posi4ve Neutral Current E2 Analysis L2 Nega4ve Neutral CurrentThursday, October 20, 2011
  51. 51. 3.2  Example  of  Metaknowledge  annota/on: S3 = These results suggest that Y has no effect on expression of X Knowledge Certainty Lexical   Event Manner Source Type Level Polarity E1 General L3 Posi4ve Neutral Current E2 Analysis L2 Nega4ve Neutral Current• Manual  annota/on  underway  of  the  GENIA  event  corpus  (1000  MEDLINE  abstracts)Thursday, October 20, 2011
  52. 52. 3.3  de  Waard/Pander  Maat:  Discourse  Segment  Types 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.Thursday, October 20, 2011
  53. 53. 3.3  de  Waard/Pander  Maat:  Discourse  Segment  Types 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.Thursday, October 20, 2011
  54. 54. 3.3  de  Waard/Pander  Maat:  Discourse  Segment  Types 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.Thursday, October 20, 2011
  55. 55. 3.3  de  Waard/Pander  Maat:  Discourse  Segment  Types 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.Thursday, October 20, 2011
  56. 56. 3.3  de  Waard/Pander  Maat:  Discourse  Segment  Types 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.Thursday, October 20, 2011
  57. 57. 3.3  de  Waard/Pander  Maat:  Discourse  Segment  Types 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.Thursday, October 20, 2011
  58. 58. 3.3  de  Waard/Pander  Maat:  Discourse  Segment  Types 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.Thursday, October 20, 2011
  59. 59. 3.3  de  Waard/Pander  Maat:  Discourse  Segment  Types 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.Thursday, October 20, 2011
  60. 60. 3.3  de  Waard/Pander  Maat:  Discourse  Segment  Types 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.Thursday, October 20, 2011
  61. 61. 3.3  de  Waard/Pander  Maat:  Discourse  Segment  Types 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.Thursday, October 20, 2011
  62. 62. 3.3  de  Waard/Pander  Maat:  Discourse  Segment  Types 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.Thursday, October 20, 2011
  63. 63. 3.3  Iden/fica/on  of  DSTs: 15Thursday, October 20, 2011
  64. 64. 3.3  Iden/fica/on  of  DSTs: -­‐ Verb  form:  tense,  e.g.   -­‐ Concepts  in  ‘state’  (gnomic)  present: ‘Dopaminergic  innerva/on  plays  a  major  role  in  the  control  of   mood  and  its  perturba/on’   -­‐ Experiments  in  ‘event’  past:   ‘Four  out  of  seven  cell  lines  expressed  this  cluster’ 15Thursday, October 20, 2011
  65. 65. 3.3  Iden/fica/on  of  DSTs: -­‐ Verb  form:  tense,  e.g.   -­‐ Concepts  in  ‘state’  (gnomic)  present: ‘Dopaminergic  innerva/on  plays  a  major  role  in  the  control  of   mood  and  its  perturba/on’   -­‐ Experiments  in  ‘event’  past:   ‘Four  out  of  seven  cell  lines  expressed  this  cluster’ -­‐ Seman4c  verb  class:   -­‐ Research  verbs  (Inves/ga/on,  Predic/on,  Procedure,   Observa/on,  Interpreta/on) -­‐ Discourse  verbs   -­‐ Proper/es  and  rela/onships  -­‐  between  things  and  concepts 15Thursday, October 20, 2011
  66. 66. 3.3  Iden/fica/on  of  DSTs: -­‐ Verb  form:  tense,  e.g.   -­‐ Concepts  in  ‘state’  (gnomic)  present: ‘Dopaminergic  innerva/on  plays  a  major  role  in  the  control  of   mood  and  its  perturba/on’   -­‐ Experiments  in  ‘event’  past:   ‘Four  out  of  seven  cell  lines  expressed  this  cluster’ -­‐ Seman4c  verb  class:   -­‐ Research  verbs  (Inves/ga/on,  Predic/on,  Procedure,   Observa/on,  Interpreta/on) -­‐ Discourse  verbs   -­‐ Proper/es  and  rela/onships  -­‐  between  things  and  concepts -­‐ Modality   -­‐ Types:  Source  {Author,  others,  unknown},  Basis  {Data,   Reasoning,  0},  Value  {Certain,  probable,  possible,  unknown} -­‐ Markers:  Modal  aux,  verb  class  Interpreta/on,  epistemic  adverbs 15Thursday, October 20, 2011
  67. 67. 3.  Same  Statement  annotated  three  ways:Thursday, October 20, 2011
  68. 68. 3.  Same  Statement  annotated  three  ways: CoreSC: <annotationART atype="GSC" type="Res" conceptID="Res24" novelty="None" advantage="None"> Here we show that BOB.1/OBF.1 regulates Btk gene expression. </annotationART> BioEvent/MetaKnowledge: <sentence id="S6">Here we show that <term id="T13" sem="Protein_family_or_group"> <gene-or-gene-product id="G9">BOB.1</gene-or-gene-product>/ <gene-or-gene-product id="G10">OBF.1</gene-or-gene-product> </term> regulates <term id="T14" sem="Biological_process"> <term id="T15" sem="DNA_domain_or_region"> <gene-or-gene-product id="G11">Btk </gene-or-gene-product> gene </term> expression </term>. </sentence> Discourse Segments: <segment segID ="286" section = "D" segtype = "RegImplication"> Here we show that </segment> <segment segID ="287" section = "D" segtype = "Implication">Thursday, October 20, 2011
  69. 69. 3.  Same  Statement  annotated  three  ways: CoreSC: <annotationART atype="GSC" type="Res" conceptID="Res24" novelty="None" advantage="None"> Here we show that BOB.1/OBF.1 regulates Btk gene expression. </annotationART> BioEvent/MetaKnowledge: <sentence id="S6">Here we show that <term id="T13" sem="Protein_family_or_group"> <gene-or-gene-product id="G9">BOB.1</gene-or-gene-product>/ <gene-or-gene-product id="G10">OBF.1</gene-or-gene-product> </term> regulates <term id="T14" sem="Biological_process"> <term id="T15" sem="DNA_domain_or_region"> <gene-or-gene-product id="G11">Btk </gene-or-gene-product> gene </term> expression </term>. </sentence> Discourse Segments: <segment segID ="286" section = "D" segtype = "RegImplication"> Here we show that </segment> <segment segID ="287" section = "D" segtype = "Implication"> BOB.1/OBF.1 regulates Btk gene expression. </segment>Thursday, October 20, 2011
  70. 70. 3.  Same  Statement  annotated  three  ways: CoreSC: <annotationART atype="GSC" type="Res" conceptID="Res24" novelty="None" advantage="None"> Here we show that BOB.1/OBF.1 regulates Btk gene expression. </annotationART> BioEvent/MetaKnowledge: <sentence id="S6">Here we show that <term id="T13" sem="Protein_family_or_group"> <gene-or-gene-product id="G9">BOB.1</gene-or-gene-product>/ <gene-or-gene-product id="G10">OBF.1</gene-or-gene-product> </term> regulates <term id="T14" sem="Biological_process"> <term id="T15" sem="DNA_domain_or_region"> <gene-or-gene-product id="G11">Btk </gene-or-gene-product> gene </term> expression </term>. </sentence> Discourse Segments: <segment segID ="286" section = "D" segtype = "RegImplication"> Here we show that </segment> <segment segID ="287" section = "D" segtype = "Implication"> BOB.1/OBF.1 regulates Btk gene expression. </segment>Thursday, October 20, 2011
  71. 71. 3.  Comparing  statement-­‐level  annota/on  models Who Why What How Liakata:  CoreSC Iden/fy  main   Sentence Manual  corpus,   components  of   automated   scien/fic  inves/ga/on   annota/on  tools  -­‐   for  machine  learning working  on   automated  detec/on Ananiadou:   Enhance  informa/on   Events  (intra-­‐ Manual  corpus,   MetaKnowledge/ extrac/on  for   senten/al):  can  be   working  on   BioEvents biomedical  texts  to   several  per   automated  detec/on enable  metadiscourse   sentence,  or  one  in   annota/on more  sentences de  Waard: Iden/fy  mechanisms   Clause Manual,  ideas  (but  no   Discourse  Segment   of  conveying   real  plans!)  for   Types (epistemic)  knowledge   automated   in  scien/fic    discourse iden/fica/onThursday, October 20, 2011
  72. 72. 4.  Rela.ons a.Why? -­‐ Argumenta/on  visualisa/on b.What,  by  whom?   -­‐ Harmsze  (1999):  Ontology  of   content  rela/onships -­‐ IBIS,  ClaiMaker  (2001) -­‐ Diligent  argumenta/on   ontology  (2005)   -­‐ SALT:  RST  (2007) -­‐ SWAN  (2010) c. How?   -­‐ So  far:  Manually 18Thursday, October 20, 2011
  73. 73. 4.  Rela.ons a.Why? -­‐ Argumenta/on  visualisa/on b.What,  by  whom?   -­‐ Harmsze  (1999):  Ontology  of   content  rela/onships -­‐ IBIS,  ClaiMaker  (2001) -­‐ Diligent  argumenta/on   ontology  (2005)   -­‐ SALT:  RST  (2007) -­‐ SWAN  (2010) c. How?   -­‐ So  far:  Manually 18Thursday, October 20, 2011
  74. 74. 4.  Rela.ons a.Why? -­‐ Argumenta/on  visualisa/on b.What,  by  whom?   -­‐ Harmsze  (1999):  Ontology  of   content  rela/onships -­‐ IBIS,  ClaiMaker  (2001) -­‐ Diligent  argumenta/on   ontology  (2005)   -­‐ SALT:  RST  (2007) -­‐ SWAN  (2010) c. How?   -­‐ So  far:  Manually 18Thursday, October 20, 2011
  75. 75. 4.  Rela.ons a.Why? -­‐ Argumenta/on  visualisa/on b.What,  by  whom?   -­‐ Harmsze  (1999):  Ontology  of   content  rela/onships -­‐ IBIS,  ClaiMaker  (2001) -­‐ Diligent  argumenta/on   ontology  (2005)   -­‐ SALT:  RST  (2007) -­‐ SWAN  (2010) c. How?   -­‐ So  far:  Manually 18Thursday, October 20, 2011
  76. 76. 4.  Rela.ons a.Why? -­‐ Argumenta/on  visualisa/on b.What,  by  whom?   -­‐ Harmsze  (1999):  Ontology  of   content  rela/onships -­‐ IBIS,  ClaiMaker  (2001) -­‐ Diligent  argumenta/on   ontology  (2005)   -­‐ SALT:  RST  (2007) -­‐ SWAN  (2010) c. How?   -­‐ So  far:  Manually 18Thursday, October 20, 2011
  77. 77. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) 19Thursday, October 20, 2011
  78. 78. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? 19Thursday, October 20, 2011
  79. 79. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work 19Thursday, October 20, 2011
  80. 80. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work b.What,  by  whom? 19Thursday, October 20, 2011
  81. 81. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work b.What,  by  whom? -­‐ Buckingham  Shum,  1999 19Thursday, October 20, 2011
  82. 82. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work b.What,  by  whom? -­‐ Buckingham  Shum,  1999 19Thursday, October 20, 2011
  83. 83. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work b.What,  by  whom? -­‐ Buckingham  Shum,  1999 -­‐ SWAN:  Clark,  Ciccarese   et  al.,  2005 19Thursday, October 20, 2011
  84. 84. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work b.What,  by  whom? -­‐ Buckingham  Shum,  1999 -­‐ SWAN:  Clark,  Ciccarese   et  al.,  2005 19Thursday, October 20, 2011
  85. 85. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work b.What,  by  whom? -­‐ Buckingham  Shum,  1999 -­‐ SWAN:  Clark,  Ciccarese   et  al.,  2005 -­‐ Nanopublica/ons:   Mons,  2010 19Thursday, October 20, 2011
  86. 86. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work b.What,  by  whom? -­‐ Buckingham  Shum,  1999 -­‐ SWAN:  Clark,  Ciccarese   et  al.,  2005 -­‐ Nanopublica/ons:   Mons,  2010 19Thursday, October 20, 2011
  87. 87. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work b.What,  by  whom? -­‐ Buckingham  Shum,  1999 -­‐ SWAN:  Clark,  Ciccarese   et  al.,  2005 -­‐ Nanopublica/ons:   Mons,  2010 -­‐ Nanopublica/ons  +   SWAN,  2011 19Thursday, October 20, 2011
  88. 88. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work b.What,  by  whom? -­‐ Buckingham  Shum,  1999 -­‐ SWAN:  Clark,  Ciccarese   et  al.,  2005 -­‐ Nanopublica/ons:   Mons,  2010 -­‐ Nanopublica/ons  +   SWAN,  2011 c.How?   19Thursday, October 20, 2011
  89. 89. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work b.What,  by  whom? -­‐ Buckingham  Shum,  1999 -­‐ SWAN:  Clark,  Ciccarese   et  al.,  2005 -­‐ Nanopublica/ons:   Mons,  2010 -­‐ Nanopublica/ons  +   SWAN,  2011 c.How?   -­‐ So  far:  manually 19Thursday, October 20, 2011
  90. 90. 5.Claim-­‐Evidence  Networks  (statement  +  rela/ons) a.Why? Show  argumenta/on   across  body  of  work b.What,  by  whom? -­‐ Buckingham  Shum,  1999 -­‐ SWAN:  Clark,  Ciccarese   et  al.,  2005 -­‐ Nanopublica/ons:   Mons,  2010 -­‐ Nanopublica/ons  +   SWAN,  2011 c.How?   -­‐ So  far:  manually 19Thursday, October 20, 2011
  91. 91. D2S  Use  case:  Claim-­‐Evidence  Network  in  Medicine B. Elsevier-publishedA. Philips’ Electronic Patient Records Clinical Guideline C. Elsevier (or other publisher’s) Research Report or Data 20Thursday, October 20, 2011
  92. 92. D2S  Use  case:  Claim-­‐Evidence  Network  in  Medicine Step 1: Patient data + diagnosis link to Guideline recommendation B. Elsevier-publishedA. Philips’ Electronic Patient Records Clinical Guideline C. Elsevier (or other publisher’s) Research Report or Data 20Thursday, October 20, 2011
  93. 93. D2S  Use  case:  Claim-­‐Evidence  Network  in  Medicine Step 1: Patient data + diagnosis link to Guideline recommendation B. Elsevier-publishedA. Philips’ Electronic Patient Records Clinical Guideline Step 2: Guideline recommendation links to evidence in report or data C. Elsevier (or other publisher’s) Research Report or Data 20Thursday, October 20, 2011
  94. 94. D2S  Use  case:  Claim-­‐Evidence  Network  in  Medicine Step 1: Patient data + diagnosis link to Guideline recommendation B. Elsevier-publishedA. Philips’ Electronic Patient Records Clinical Guideline Step 2: Guideline recommendation links to evidence in report or data C. Elsevier (or other publisher’s) Research Report or Data Related  HCLS  Use  Case:  Accelerate  uptake  of  medical  research   on  drug-­‐drug  interac/on  in  product  inserts 20Thursday, October 20, 2011
  95. 95. Five  levels  of  scien/fic  discourse  annota/on 21Thursday, October 20, 2011
  96. 96. Five  levels  of  scien/fic  discourse  annota/on Why What/Who How Automated!   Sec/on Search,  UI ABCDE,  ORB/HCLS Publisher  helps?   Harmsze/Kircz,  LiquidPub,   Module Content  reuse HCLS Manual:  templates Teufel,  Ananiadou,   Summaries;   Working  towards   Statement towards  networks Liakata,   automated  detec/on UU SALT,  ScholOnto,  Diligent,   Manual:  some  tools,   Rela/ons Networks SWAN never  took  off... Claim/ Argumenta/on    ScholOnto,  SWAN,   Manual-­‐  towards   Evidence networks Nanopublica/ons,  D2S automa/on?   21Thursday, October 20, 2011
  97. 97. Five  levels  of  scien/fic  discourse  annota/on Why What/Who How Automated!   Sec/on Search,  UI ABCDE,  ORB/HCLS Publisher  helps?   Harmsze/Kircz,  LiquidPub,   Module Content  reuse HCLS Manual:  templates Teufel,  Ananiadou,   Summaries;   Working  towards   Statement towards  networks Liakata,   automated  detec/on UU SALT,  ScholOnto,  Diligent,   Manual:  some  tools,   Rela/ons Networks SWAN never  took  off... Claim/ Argumenta/on    ScholOnto,  SWAN,   Manual-­‐  towards   Evidence networks Nanopublica/ons,  D2S automa/on?   21Thursday, October 20, 2011
  98. 98. Five  levels  of  scien/fic  discourse  annota/on Why What/Who How Automated!   Sec/on Search,  UI ABCDE,  ORB/HCLS Publisher  helps?   Harmsze/Kircz,  LiquidPub,   Module Content  reuse HCLS Manual:  templates Teufel,  Ananiadou,   Summaries;   Working  towards   Statement towards  networks Liakata,   automated  detec/on UU SALT,  ScholOnto,  Diligent,   Manual:  some  tools,   Rela/ons Networks SWAN never  took  off... Claim/ Argumenta/on    ScholOnto,  SWAN,   Manual-­‐  towards   Evidence networks Nanopublica/ons,  D2S automa/on?   21Thursday, October 20, 2011
  99. 99. Five  levels  of  scien/fic  discourse  annota/on Why What/Who How Automated!   Sec/on Search,  UI ABCDE,  ORB/HCLS Publisher  helps?   Harmsze/Kircz,  LiquidPub,   Module Content  reuse HCLS Manual:  templates Teufel,  Ananiadou,   Summaries;   Working  towards   Statement towards  networks Liakata,   automated  detec/on UU SALT,  ScholOnto,  Diligent,   Manual:  some  tools,   Rela/ons Networks SWAN never  took  off... Claim/ Argumenta/on    ScholOnto,  SWAN,   Manual-­‐  towards   Evidence networks Nanopublica/ons,  D2S automa/on?   21Thursday, October 20, 2011
  100. 100. Five  levels  of  scien/fic  discourse  annota/on Why What/Who How Automated!   Sec/on Search,  UI ABCDE,  ORB/HCLS Publisher  helps?   Harmsze/Kircz,  LiquidPub,   Module Content  reuse HCLS Manual:  templates Teufel,  Ananiadou,   Summaries;   Working  towards   Statement towards  networks Liakata,   automated  detec/on UU SALT,  ScholOnto,  Diligent,   Manual:  some  tools,   Rela/ons Networks SWAN never  took  off... Claim/ Argumenta/on    ScholOnto,  SWAN,   Manual-­‐  towards   Evidence networks Nanopublica/ons,  D2S automa/on?   21Thursday, October 20, 2011
  101. 101. Five  levels  of  scien/fic  discourse  annota/on Why What/Who How Automated!   Sec/on Search,  UI ABCDE,  ORB/HCLS Publisher  helps?   Harmsze/Kircz,  LiquidPub,   Module Content  reuse HCLS Manual:  templates Teufel,  Ananiadou,   Summaries;   Working  towards   Statement towards  networks Liakata,   automated  detec/on UU SALT,  ScholOnto,  Diligent,   Manual:  some  tools,   Rela/ons Networks SWAN never  took  off... Claim/ Argumenta/on    ScholOnto,  SWAN,   Manual-­‐  towards   Evidence networks Nanopublica/ons,  D2S automa/on?   21Thursday, October 20, 2011
  102. 102. Five  levels  of  scien/fic  discourse  annota/on Why What/Who How Automated!   Sec/on Search,  UI ABCDE,  ORB/HCLS Publisher  helps?   Harmsze/Kircz,  LiquidPub,   Module Content  reuse HCLS Manual:  templates MoFfs?   Teufel,  Ananiadou,   Summaries;   Working  towards   Statement towards  networks Liakata,   automated  detec/on UU SALT,  ScholOnto,  Diligent,   Manual:  some  tools,   Rela/ons Networks SWAN never  took  off... Claim/ Argumenta/on    ScholOnto,  SWAN,   Manual-­‐  towards   Evidence networks Nanopublica/ons,  D2S automa/on?   21Thursday, October 20, 2011
  103. 103. Ques.ons: 22Thursday, October 20, 2011
  104. 104. Ques.ons: Scien/fic  discourse  -­‐>  fairy  tales:  how  can  we  transfer  knowledge   here  to  scien/fic  discourse  community?   22Thursday, October 20, 2011
  105. 105. Ques.ons: Scien/fic  discourse  -­‐>  fairy  tales:  how  can  we  transfer  knowledge   here  to  scien/fic  discourse  community?   Issue:  Scien/sts  do  not  like  being  told  that  they  write  fairy  tales! 22Thursday, October 20, 2011
  106. 106. Ques.ons: Scien/fic  discourse  -­‐>  fairy  tales:  how  can  we  transfer  knowledge   here  to  scien/fic  discourse  community?   Issue:  Scien/sts  do  not  like  being  told  that  they  write  fairy  tales! Fairy  tales  -­‐>  scien/fic  discourse:  is  anyone  here/in  this  community   interested  in  working  on  inter-­‐domain  transfer  of  tools,   technologies  and  theories? 22Thursday, October 20, 2011
  107. 107. Ques.ons: Scien/fic  discourse  -­‐>  fairy  tales:  how  can  we  transfer  knowledge   here  to  scien/fic  discourse  community?   Issue:  Scien/sts  do  not  like  being  told  that  they  write  fairy  tales! Fairy  tales  -­‐>  scien/fic  discourse:  is  anyone  here/in  this  community   interested  in  working  on  inter-­‐domain  transfer  of  tools,   technologies  and  theories? Anita  de  Waard,  a.dewaard@elsevier.com   -­‐HCLS:  hEp://www.w3.org/wiki/HCLSIG/SWANSIOC -­‐UU:  hEp://elsatglabs.com/labs/anita   -­‐D2S:  hEp://www.data2seman/cs.org 22Thursday, October 20, 2011

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