On the research paper, and the knowledge within

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Presentation on May 4th, 2011 at MITRE on Stories that persuade with Data; expanded version of talk at Harvard 'Reengineering the research paper'.

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On the research paper, and the knowledge within

  1. 1. Stories, that persuade with data: On the research paper, and the knowledge within 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 grammar of fairytales:
  5. 5. Story grammar of fairytales:According to Propp, main characters (or dramatis personae)that are occuring in a fairy tale may be the following:1. Hero: a character that seeks something;2. Villain: opposes or actively blocks the heroʼs quest;3. Donor: provides the hero with an object of magicalproperties;4. Dispatcher: sends the hero on his/her quest via a message;5. False Hero: disrupts the heroʼs success by making falseclaims;6. Helper: aids the hero;7. Princess: acts as the reward for the hero and the object ofthe villainʼs plots;8. Her Father: acts to reward the hero for his effort.
  6. 6. Story grammar of fairytales: F. Peinado, P. Gervas, and B. Diaz-Agudo, ʻA description logic ontology for fairy tale generationʼ, in Procs LREC. ELRA, (5 2004)According to Propp, main characters (or dramatis personae)that are occuring in a fairy tale may be the following:1. Hero: a character that seeks something;2. Villain: opposes or actively blocks the heroʼs quest;3. Donor: provides the hero with an object of magicalproperties;4. Dispatcher: sends the hero on his/her quest via a message;5. False Hero: disrupts the heroʼs success by making falseclaims;6. Helper: aids the hero;7. Princess: acts as the reward for the hero and the object ofthe villainʼs plots;8. Her Father: acts to reward the hero for his effort.
  7. 7. Story grammar of fairytales: F. Peinado, P. Gervas, and B. Diaz-Agudo, ʻA description logic ontology for fairy tale generationʼ, in Procs LREC. ELRA, (5 2004)According to Propp, main characters (or dramatis personae)that are occuring in a fairy tale may be the following:1. Hero: a character that seeks something;2. Villain: opposes or actively blocks the heroʼs quest;3. Donor: provides the hero with an object of magicalproperties;4. Dispatcher: sends the hero on his/her quest via a message;5. False Hero: disrupts the heroʼs success by making falseclaims;6. Helper: aids the hero;7. Princess: acts as the reward for the hero and the object ofthe villainʼs plots;8. Her Father: acts to reward the hero for his effort.
  8. 8. Story analysis of scientific text:ORB vs. Medium-grained structure
  9. 9. Story analysis of scientific text: ORB vs. Medium-grained structureSee work at http://www.w3.org/wiki/HCLSIG/SWANSIOC
  10. 10. Episode-level access through Linked Data standards:
  11. 11. Episode-level access through Linked Data standards:<ce:section id=#123>
  12. 12. Episode-level access through Linked Data standards: this says<ce:section id=#123> mice like cheese
  13. 13. Episode-level access through Linked Data standards: said @anita on April 5, 2011 this says<ce:section id=#123> mice like cheese
  14. 14. 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
  15. 15. Episode-level access through Linked Data standards:the xml is fixed, but the structure is open! but we all know she was deluded then said @anita on April 5, 2011 this says <ce:section id=#123> mice like cheese
  16. 16. 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
  17. 17. Satellite Format: LDR store for all our content
  18. 18. Satellites: ProvenanceInformation about an annotation: -Who created it?,When? By what (version of a) tool? -Has it been reviewed? If so, when and by whom? Was it approved or rejected?Use pav:createdOn and createdBy instead of dc:date and creator to reduceconfusion:<tag:TaggingAnnotation rdf:about="#anno-1"> <tag:annotatesStatement rdf:resource="#stmt-1"/> <tag:score>0.8939283</tag:score><pav:createdOn>2010-07-23T15:45:00Z</pav:createdOn><pav:createdBy rdf:resource= "http://data.elsevier.com/enh-services/ProjectCode/version"/> <tag:status rdf:resource= "http://data.elsevier.com/namespace/LDR-Satellite/TagAnnot-1/ VendorChecked"/></tag:TaggingAnnotation>
  19. 19. Satellites: FragmentsUse XPointer for XML documents, Media Fragments for image, video, audio.XMLDocumentRegion, MediaRegion akin to Annotation Ontology Selectorsxpath1()* XPointer scheme so pointer can be dropped into any XPath engine andget back the section being annotated.Complex case – arbitrary string in document:<rgn:XMLDocumentRegion rdf: about= "http://.../S0140-6736(95)90494-8#xpath-e(substring(id(sb-3)/p[2],15,6))"> <dct:isPartOf rdf:resource="http://.../S0140-6736(95)90494-8"/> <rgn:coveringXPath>id(sb-3)/p[2]</rgn:coveringXPath> <rgn:startingOffset>15</rgn:startingOffset> <rgn:stringLength>6</rgn:stringLength> <rgn:matchedString>biopsy</rgn:matchedString> <rgn:prefixString>Testing of the </rgn:prefixString> <rgn:suffixString>indicated nothing</rgn:suffixString></rgn:XMLDocumentRegion>
  20. 20. 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.
  21. 21. 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.
  22. 22. 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.
  23. 23. 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.
  24. 24. 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.
  25. 25. Realms of persuasive experimental discourse:
  26. 26. 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),
  27. 27. 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
  28. 28. 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
  29. 29. 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,
  30. 30. 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,
  31. 31. 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
  32. 32. 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).
  33. 33. 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).
  34. 34. 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)
  35. 35. 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)
  36. 36. “[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
  37. 37. “[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
  38. 38. The logical structure of a scientific claim
  39. 39. The logical structure of a scientific claim- A Proposition P is about entities, relations, events, actions…
  40. 40. The logical structure of a scientific claim- A Proposition P is about entities, relations, events, actions…- We define an Epistemic Evaluation of P to be EEs,v(P): - S = Source = Holder, Basis: - Holder: Author (A), Referent (N), Nameless referent (NN) - Basis: Reasoning (R), Data (D), Unidentified (Ø) - V = Value = Certainly, Emphasis: - Certainty: from 0 (uncertainty) to 3 (complete certainty) - Emphasis: Focus (F: +/-), Surprise (S, +,-)
  41. 41. The logical structure of a scientific claim- A Proposition P is about entities, relations, events, actions…- We define an Epistemic Evaluation of P to be EEs,v(P): - S = Source = Holder, Basis: - Holder: Author (A), Referent (N), Nameless referent (NN) - Basis: Reasoning (R), Data (D), Unidentified (Ø) - V = Value = Certainly, Emphasis: - Certainty: from 0 (uncertainty) to 3 (complete certainty) - Emphasis: Focus (F: +/-), Surprise (S, +,-)- Nested evaluations, e.g. “We question X’s suggestion that P” can be written as: EEA(EE’N(P)).
  42. 42. The logical structure of a scientific claim- A Proposition P is about entities, relations, events, actions…- We define an Epistemic Evaluation of P to be EEs,v(P): - S = Source = Holder, Basis: - Holder: Author (A), Referent (N), Nameless referent (NN) - Basis: Reasoning (R), Data (D), Unidentified (Ø) - V = Value = Certainly, Emphasis: - Certainty: from 0 (uncertainty) to 3 (complete certainty) - Emphasis: Focus (F: +/-), Surprise (S, +,-)- Nested evaluations, e.g. “We question X’s suggestion that P” can be written as: EEA(EE’N(P)).- If no explicit evaluation (“Water is wet”), of course, EE = Ø.
  43. 43. 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 upregulated N, D 3work on neutrophils by interferons in vitro [..]}Offer it is thought that {these transcription factors affect NN, R 2hypotheses 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 of Since {this was not the case with other lines,} {we A, D 1interpretations suspect {it is integration-site specific}}State While we expected {the transcript to be about 1 kb A, D 2, S+correspondence 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/D specific promoters,}}
  44. 44. One application: improve text mining:insulin ::: maintaining glucose ... diabetes defect) to overcomeGB00084 homeostasis insulin resistance in maintaining1 glucose homeostasis, hyperglycemia and glucose intolerance ... improve glucose ... in T2D is able to increase homeostasis insulin secretion and improve glucose homeostasis. improves glucose ... SIRT1, whose administration homeostasis to insulin-resistant animals improves glucose homeostasis. is capable glucose S15511 is a novel insulin homeostasis sensitizer that is capable of improving glucose homeostasis in nondiabetic rats. maintains glucose Pancreatic beta-cells possess a homeostasis well-regulated insulin secretory property that maintains systemic glucose homeostasis. may be glucose ... similar way to those of involved homeostasis insulin, PANDER may be involved in glucose homeostasis. participates glucose Fine-tuning of insulin secretion homeostasis from pancreatic beta-cells participates in blood glucose homeostasis.
  45. 45. One application: improve text mining:insulin ::: maintaining glucose ... diabetes defect) to overcome When insulin secretion cannot be increased adequately (type I diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis,GB00084 homeostasis insulin resistance in maintaining hyperglycemia and glucose intolerance ensues. Insulin resistance and glucose1 glucose homeostasis, intolerance has been well recognized in patients with advanced hyperglycemia and glucose chronic kidney diseases (CKD). intolerance ... improve glucose ... in T2D is able to increase .. Incretin metabolism is abnormal in T2D, evidenced by a decreased incretin effect, reduction in nutrient-mediated secretion of GIP and GLP-1 in homeostasis insulin secretion and improve T2D, and resistance to GIP. GLP-1, on the other hand, when administered glucose homeostasis. intravenously in T2D is able to increase insulin secretion and improve glucose homeostasis. improves glucose ... SIRT1, whose administration SIRT1, a NAD(+)-dependent protein deacetylase that regulates transcription factors involved in key cellular processes, has been implicated as a mediator homeostasis to insulin-resistant animals of the beneficial effects of calorie restriction. In a recent issue of Nature, improves glucose homeostasis. Milne et al. (2007) describe novel potent activators of SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis. is capable glucose S15511 is a novel insulin S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.... However, the mechanisms behind the insulin- homeostasis sensitizer that is capable of sensitizing effect of S15511 are unknown. The aim of our study was improving glucose homeostasis to explore whether S15511 improves insulin sensitivity in skeletal in nondiabetic rats. muscles. S15511 treatment was associated with an increase in insulin- stimulated glucose transport in type IIb fibers, while type I fibers were unaffected. maintains glucose Pancreatic beta-cells possess a Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis. Although it has long been homeostasis well-regulated insulin secretory thought that differentiated beta-cells are nearly static, recent studies property that maintains have shown that beta-cell mass dynamically changes throughout the systemic glucose homeostasis. lifetime. In this article, recent progress of regenerative medicine of the pancreas is reviewed. may be glucose ... similar way to those of ... Our results showed that glucose up-regulated PANDER mRNA and involved homeostasis insulin, PANDER may be protein levels in a time- and dose-dependent manner in MIN6 cells and pancreatic islets. ...Because PANDER is expressed by pancreatic beta-cells involved in glucose homeostasis. and in response to glucose in a similar way to those of insulin, PANDER may be involved in glucose homeostasis. participates glucose Fine-tuning of insulin secretion Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood homeostasis from pancreatic beta-cells glucose homeostasis. ... Our data identify miR124a and miR96 as novel regulators of the expression of proteins playing a critical role in insulin participates in blood glucose exocytosis and in the release of other hormones and neurotransmitters. homeostasis.
  46. 46. One application: improve text mining:insulin ::: maintaining glucose ... diabetes defect) to overcome When insulin secretion cannot be increased adequately (type I diabetes defect) to overcome insulin resistance in maintaining glucose homeostasis,GB00084 homeostasis insulin resistance in maintaining hyperglycemia and glucose intolerance ensues. Insulin resistance and glucose1 glucose homeostasis, intolerance has been well recognized in patients with advanced hyperglycemia and glucose chronic kidney diseases (CKD). intolerance ... improve glucose ... in T2D is able to increase .. Incretin metabolism is abnormal in T2D, evidenced by a decreased incretin effect, reduction in nutrient-mediated secretion of GIP and GLP-1 in homeostasis insulin secretion and improve T2D, and resistance to GIP. GLP-1, on the other hand, when administered glucose homeostasis. intravenously in T2D is able to increase insulin secretion and improve glucose homeostasis. improves glucose ... SIRT1, whose administration SIRT1, a NAD(+)-dependent protein deacetylase that regulates transcription factors involved in key cellular processes, has been implicated as a mediator homeostasis to insulin-resistant animals of the beneficial effects of calorie restriction. In a recent issue of Nature, improves glucose homeostasis. Milne et al. (2007) describe novel potent activators of SIRT1, whose administration to insulin-resistant animals improves glucose homeostasis. is capable glucose S15511 is a novel insulin S15511 is a novel insulin sensitizer that is capable of improving glucose homeostasis in nondiabetic rats.... However, the mechanisms behind the insulin- homeostasis sensitizer that is capable of sensitizing effect of S15511 are unknown. The aim of our study was improving glucose homeostasis to explore whether S15511 improves insulin sensitivity in skeletal in nondiabetic rats. muscles. S15511 treatment was associated with an increase in insulin- stimulated glucose transport in type IIb fibers, while type I fibers were unaffected. maintains glucose Pancreatic beta-cells possess a Pancreatic beta-cells possess a well-regulated insulin secretory property that maintains systemic glucose homeostasis. Although it has long been homeostasis well-regulated insulin secretory thought that differentiated beta-cells are nearly static, recent studies property that maintains have shown that beta-cell mass dynamically changes throughout the systemic glucose homeostasis. lifetime. In this article, recent progress of regenerative medicine of the pancreas is reviewed. may be glucose ... similar way to those of ... Our results showed that glucose up-regulated PANDER mRNA and involved homeostasis insulin, PANDER may be protein levels in a time- and dose-dependent manner in MIN6 cells and pancreatic islets. ...Because PANDER is expressed by pancreatic beta-cells involved in glucose homeostasis. and in response to glucose in a similar way to those of insulin, PANDER may be involved in glucose homeostasis. participates glucose Fine-tuning of insulin secretion Fine-tuning of insulin secretion from pancreatic beta-cells participates in blood homeostasis from pancreatic beta-cells glucose homeostasis. ... Our data identify miR124a and miR96 as novel regulators of the expression of proteins playing a critical role in insulin participates in blood glucose exocytosis and in the release of other hormones and neurotransmitters. homeostasis.
  47. 47. Other application: improve citations ! Model of phenomenon time = t+1 ? Model of phenomenon time = tDomain Model (C) Ed Hovy
  48. 48. Other application: improve citations ! Model of phenomenon time = t+1 ? Model of phenomenon time = tDomain Model (C) Ed Hovy
  49. 49. Other application: improve citations ! Model of phenomenon time = t+1 ? Citation: Model of phenomenon • ‘Lifts’ claim from previous paper and add it to current paper time = t • We need ‘rules for legal lifting’: • Express author’s claim trulyDomain Model • Maintain (experimental) content • Apply appropriately (C) Ed Hovy
  50. 50. Other application: improve citations ! Model of phenomenon time = t+1 ? Citation: Model of phenomenon • ‘Lifts’ claim from previous paper and add it to current paper time = t • We need ‘rules for legal lifting’: • Express author’s claim trulyDomain Model • Maintain (experimental) content • Apply appropriately What does this mean? (C) Ed Hovy
  51. 51. Eventually: trace roots of a claim:how many independent data points is it based on? 17
  52. 52. Eventually: trace roots of a claim:how many independent data points is it based on? PHC undergo Growth arrest 17
  53. 53. 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 17
  54. 54. 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 17
  55. 55. 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 17
  56. 56. 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 17
  57. 57. 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 17
  58. 58. 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 17
  59. 59. 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 17
  60. 60. 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 17
  61. 61. Scientific papers are stories,that persuade with data.
  62. 62. Scientific papers are stories,that persuade with data.
  63. 63. Scientific papers are stories,that persuade with data.
  64. 64. Sometimes the link to data is good:
  65. 65. And sometimes it’s not so good:
  66. 66. And sometimes it’s not so good:
  67. 67. And sometimes it’s not so good:
  68. 68. And sometimes it’s not so good:
  69. 69. Can we make data-driven papers? Work done with Ed Hovy, Phil Bourne, Gully Burns and Cartic Ramakrishnan
  70. 70. Can we make 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
  71. 71. Can we make 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
  72. 72. Can we make 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-
  73. 73. Can we make 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
  74. 74. Can we make 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
  75. 75. Can we make 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 publisher Review Revise Edit
  76. 76. One step: encouraging submission of structured workflows
  77. 77. Another step: ScienceDirect app store
  78. 78. Another step: ScienceDirect app store - Eclipse SDK platform accessing all ScienceDirect/Scopus content - Build applications on top of content - Offer to users in marketplace
  79. 79. 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
  80. 80. 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
  81. 81. In Summary:
  82. 82. In Summary:1. Stories: - ORB, Satellite: link to any part of content - bring it on!
  83. 83. 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
  84. 84. 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.
  85. 85. 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?
  86. 86. 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
  87. 87. 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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