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SADI, SHARE and the Scientific Method<br />The Quest for the Holy Grail<br />
The Problem<br />
The Problem<br />
The Holy Grail:(this slide created circa 2002)<br />Align the promoters of all serine threoninekinases involved exclusivel...
Two novel technologies <br />developed in our lab<br />are getting us very close to the Holy Grail!<br />
Holy Grail Demo #1<br />
Imagine there is a “virtual database” containing all of the data from all of the databases,together with the output ofever...
How do we query that database?<br />
A Brief Digression…<br />
“Database”<br />
?<br />
Boxes became ovals…<br />Straight lines became curvy lines…<br />
Boxes became ovals…<br />Straight lines became curvy lines…<br />…and you want us to give you a grant for THAT??<br />
Relational Database<br />“Graph”<br />
Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Type ID<br />Protein Table<br />-----------------...
“Foreign keys” are used to link tables in a database<br />Gene Table<br />-----------------------<br />Gene ID<br />Tissue...
Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Type ID<br />Protein Table<br />-----------------...
Both Data Sources are on the Same Machine<br />Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Ty...
Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Type ID<br />Protein Table<br />-----------------...
“Meaning” of the connection between data-points is understood only by the database administrator<br />Protein regulates Ge...
Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Type ID<br />Protein Table<br />-----------------...
Connect all of the graphs in the world <br />to one another<br />And what do you get?<br />
Mark Butler (2003) Is the semantic web hype? Hewlett Packard laboratories presentation at MMU, 2003-03-12<br />
The lavender portion represents biology – currently ~40,000,000,000 Triples(we and our collaborators will be doubling that...
How do you find information on this<br />“Semantic Web”<br />??<br />
SPARQL<br />The query language used to discover and extract information represented in Graphs<br />
SPARQL<br />Unfortunately, YOU have to know which Web resources contain which Triples<br />(HARD!)<br />Even if you do kno...
SPARQL<br />If the data doesn’t existin any Graph at all…<br />
Basically…<br />A novel way of making Triples available on the Semantic Web, using a technology called Web Services<br />“...
Basically…<br />We invented SADI to overcome some/all of these problems<br />…but I wont bore you with the technical detai...
Detour EndsPlease resume speed<br />
Holy Grail Demo #1<br />Imagine there is a “virtual database” containing all of the data from all of the databases,togethe...
SHARESemantic Health And Research Environment<br />SPARQL enhanced by SADI<br />
A  Novel SPARQL Query Engine<br />Overcomes some of the limitations of traditional SPARQL query-handlers<br />
A  Novel SPARQL Query Engine<br />Overcomes some of the limitations of traditional SPARQL query-handlers<br />…and more…<b...
A  Novel SPARQL Query Engine<br />Overcomes some of the limitations of traditional SPARQL query-handlers<br />…and more…<b...
What pathways does UniProt protein P47989 belong to?<br />PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl...
What pathways does UniProt protein P47989 belong to?<br />PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl...
What pathways does UniProt protein P47989 belong to?<br />PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl...
Now stick that query into SHARE<br />
Recapwhat we just saw<br />A standard SPARQL query was entered into SHARE, a SADI-aware query engine<br />
Recapwhat we just saw<br />The query was interpreted to extract the individual data/relationships being requested <br />(a...
Recapwhat we just saw<br />The “triple-patterns” required to answer the query are passed to SADI for Web Service discovery...
Recapwhat we just saw<br />Services capable of generating those triple-patterns are automatically executed, the triples ar...
Recapwhat we just saw<br />We posed, and answered a ~complex database query <br />WITHOUT A DATABASE<br />(in fact, the da...
Holy Grail Demo #1<br />Align the promoters of all serine threonine kinases involved exclusively in the regulation of cell...
Holy Grail Demo #2<br />
Show me the latest Blood Urea Nitrogen and Creatinine levelsof patients who appear to be rejecting their transplants<br />...
Likely Rejecter:<br />A patient who has creatinine levelsthat are increasing over time<br />- - Wilkinson MD<br />
Likely Rejecter:<br />…but there is no “likely rejecter” column or table in our database… only blood chemistry measurement...
?<br />
The definition of a LikelyRejecter is encoded in a machine-readable document  written in the OWL language  (“Ontology”)<br...
The machine continues to burrow down through the definition and discovers that regression lines have things like slopes an...
Then… <br />Two magical events occur…<br />
The machine figures out<br />by itselfthe need to do a Linear Regression analysisin order to answer your question<br />
The machine figures out<br />by itselfhow and wherethat analysiscan be doneand does it automatically!<br />
http://www.impactlab.net/2009/03/22/improve-your-brain-power/<br />
The SHARE system utilizes SADI to discover analytical services on the Web that do linear regression analysis<br />
VOILA!<br />
How do we do that?!?<br />We let the data describe itself!<br />This is a different frommost of the bioinformatics world,w...
Data exhibits “late binding”<br />
Late binding:“purpose and meaning”of the data isnot determined untilthe moment it is required<br />
Benefit<br />of late binding<br />Data is amenable to<br />constant re-interpretation<br />
Example?<br />Blood Creatinine measurements<br />were not dictated to be (only)<br />Blood Creatinine measurements!<br />
Example?<br />The data had the ‘qualities/properties’ that<br />allowed the machine to infer<br />that they were Blood Cre...
Example?<br />But the data also had the ‘qualities/properties’ that <br />allowed them to be interpreted as <br />X/Y coor...
http://www.flickr.com/people/faernworks/<br />
Holy Grail Demo #2<br />Align the promoters of all serine threonine kinases involved exclusively in the regulation of cell...
The Holy Grail may not yet be in-handbut we can at least see it from here!So… now what?<br />
Mark’s Manifesto<br />What is my next “Holy Grail”?<br />
Science<br />Support for the in silico<br />Scientific Method<br />
The Scientific Method<br />Discourse:  What do you believe?  What do I believe?<br />Disagreement:  You’re wrong!  And I’m...
The Scientific Method<br />Discourse:  What do you believe?  What do I believe?<br />Disagreement:  You’re wrong!  And I’m...
Another Brief Digression…<br />
“Facebook” for Scientists<br />http://myexperiment.org<br />
An exciting evolution in the way Researchers express and share their in silico “Materials and Methods”<br />Through things...
Workflows are explicit representationsof the method by which an analysis was doneand which resources are used to do it<br />
Workflows can be very simple…<br />   “Blast this sequence”<br />
Or not...<br />This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which r...
Why bother?<br />
Taverna<br />A workbench for designing and executingScientific Workflows<br />
Load-up your data and press “play”!<br />…Then go home for the weekend!  You are just one click away from your M.Sc.!!<br />
By the by…<br />The SHARE application automatically creates a Workflow and then automatically runs it.This is where the da...
Detour EndsPlease resume speed<br />
WORKFLOWS<br />
At the moment <br />the Semantic Web in Healthcare and Life Sciencesaddresses these issues by attempting to create “consen...
Large, centralized ontologies <br />(e.g. the Gene Ontology)<br />that claim to represent community agreement about “biolo...
…is that Science?<br />
To restore the “traditions of Science” to in silico science<br />The Semantic Web needs to encourage/facilitate personal o...
What has this got to do with SADI and SHARE?<br />
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> <br />PREFIX patient: <http://sadiframework.org/ontologies/patie...
Likely Rejecter<br />
I created a small ontology describing my definition ofa Likely Rejecter<br />
… it was MY ontology!<br />
I can re-use it<br />
I can modify it as I change myworld-view<br />
I can publish it for others to use<br />
Others can modify it and/or compare it to THEIR world-view<br />
Sharing my ontology gives opportunities for “micro-attribution”“Credit” to me is automatic when someone uses my ontology i...
Using SADI and SHAREmypersonal world-view isexplicitlyexpressedand can bedynamically evaluated againstglobal data and know...
http://www.dailymail.co.uk/femail/article-488234/Friends-dignity-self-respect---weight-wasnt-I-lost-slimming-club.html<br />
…but there’s more…<br />
“Likely Rejecter”<br />
I made that up!  It came out of my head!<br />
What’s another word for a world-view that you make-up?<br />Hypothesis<br />
The “Likely Rejecter” OWL Class<br />is an explicitly-expressed hypothesis;<br />Members of that class may or may not exis...
Ontologically-expressed Hypotheses drive the discovery, assembly, and analysis of data capable of evaluating their validit...
Join us!<br />SADI and CardioSHARE are Open-Source projects<br />Come join us – we’re having a lot of fun!!<br />http://sa...
 Credits<br />Benjamin VanderValk(SHARE & SADI)<br />Luke McCarthy (SADI, SHARE, Taverna, CardioSHARE)<br />SoroushSamadia...
U of New Brunswick<br />Dr. Chris BakerAlexandreRiazanov<br />Carleton University<br />Dr. Michel Dumontier<br />	Marc-Ale...
Microsoft Research<br />
                          Credits<br />Benjamin VanderValk (SADI & CardioSHARE)<br />Luke McCarthy (SADI & CardioSHARE)<br...
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The Scientific Method on the Semantic Web

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Transcript of "The Scientific Method on the Semantic Web"

  1. 1. SADI, SHARE and the Scientific Method<br />The Quest for the Holy Grail<br />
  2. 2. The Problem<br />
  3. 3. The Problem<br />
  4. 4. The Holy Grail:(this slide created circa 2002)<br />Align the promoters of all serine threoninekinases involved exclusively in the regulation of cell sorting during wound healing in blood vessels.<br />Retrieve and align 2000nt 5' from every serine/threonine kinase in Mus musculus expressed exclusively in the tunica [I | M |A] whose expression increases 5X or more within 5 hours of wounding but is not activated during the normal development of blood vessels, and is <40% homologous in the active site to kinases known to be involved in cell-cycle regulation in any other species.<br />
  5. 5. Two novel technologies <br />developed in our lab<br />are getting us very close to the Holy Grail!<br />
  6. 6. Holy Grail Demo #1<br />
  7. 7. Imagine there is a “virtual database” containing all of the data from all of the databases,together with the output ofevery conceivable analysis<br />
  8. 8. How do we query that database?<br />
  9. 9. A Brief Digression…<br />
  10. 10. “Database”<br />
  11. 11.
  12. 12.
  13. 13.
  14. 14. ?<br />
  15. 15. Boxes became ovals…<br />Straight lines became curvy lines…<br />
  16. 16. Boxes became ovals…<br />Straight lines became curvy lines…<br />…and you want us to give you a grant for THAT??<br />
  17. 17. Relational Database<br />“Graph”<br />
  18. 18. Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Type ID<br />Protein Table<br />-----------------------<br />Protein Index<br />Protein Name<br />Regulates ID<br />isRepressorOf<br />http://ncbi.nlm/NR/NR_14487<br />http://pdb.org/114487<br />
  19. 19. “Foreign keys” are used to link tables in a database<br />Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Type ID<br />Protein Table<br />-----------------------<br />Protein Index<br />Protein Name<br />Regulates ID<br />isRepressorOf<br />http://ncbi.nlm/NR/NR_14487<br />http://pdb.org/114487<br />
  20. 20. Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Type ID<br />Protein Table<br />-----------------------<br />Protein Index<br />Protein Name<br />Regulates ID<br />Links in Graphs consist of statements called“TRIPLES” <br />isRepressorOf<br />http://ncbi.nlm/NR/NR_14487<br />http://pdb.org/114487<br />
  21. 21. Both Data Sources are on the Same Machine<br />Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Type ID<br />Protein Table<br />-----------------------<br />Protein Index<br />Protein Name<br />Regulates ID<br />isRepressorOf<br />http://ncbi.nlm/NR/NR_14487<br />http://pdb.org/114487<br />
  22. 22. Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Type ID<br />Protein Table<br />-----------------------<br />Protein Index<br />Protein Name<br />Regulates ID<br />Graph Data Sources (may be) on Independent Machines on the Web<br />isRepressorOf<br />http://ncbi.nlm/NR/NR_14487<br />http://pdb.org/114487<br />
  23. 23. “Meaning” of the connection between data-points is understood only by the database administrator<br />Protein regulates Gene<br />Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Type ID<br />Protein Table<br />-----------------------<br />Protein Index<br />Protein Name<br />Regulates ID<br />isRepressorOf<br />http://ncbi.nlm/NR/NR_14487<br />http://pdb.org/114487<br />
  24. 24. Gene Table<br />-----------------------<br />Gene ID<br />Tissue ID<br />Type ID<br />Protein Table<br />-----------------------<br />Protein Index<br />Protein Name<br />Regulates ID<br />“Meaning” of the connection in a Graph is explicitly labeled(and machine-readable!)<br />isRepressorOf<br />http://ncbi.nlm/NR/NR_14487<br />http://pdb.org/114487<br />
  25. 25. Connect all of the graphs in the world <br />to one another<br />And what do you get?<br />
  26. 26. Mark Butler (2003) Is the semantic web hype? Hewlett Packard laboratories presentation at MMU, 2003-03-12<br />
  27. 27. The lavender portion represents biology – currently ~40,000,000,000 Triples(we and our collaborators will be doubling that number in the next 12 months)<br />
  28. 28. How do you find information on this<br />“Semantic Web”<br />??<br />
  29. 29. SPARQL<br />The query language used to discover and extract information represented in Graphs<br />
  30. 30. SPARQL<br />Unfortunately, YOU have to know which Web resources contain which Triples<br />(HARD!)<br />Even if you do know this, SPARQL has significant limitations when attempting to query over disparate Graphs<br />(SLOW AND CUMBERSOME)<br />
  31. 31. SPARQL<br />If the data doesn’t existin any Graph at all…<br />
  32. 32.
  33. 33. Basically…<br />A novel way of making Triples available on the Semantic Web, using a technology called Web Services<br />“Services” for short<br />
  34. 34. Basically…<br />We invented SADI to overcome some/all of these problems<br />…but I wont bore you with the technical details…<br />
  35. 35. Detour EndsPlease resume speed<br />
  36. 36. Holy Grail Demo #1<br />Imagine there is a “virtual database” containing all of the data from all of the databases,together with the output ofevery conceivable analysis<br />How do we query that database? <br />
  37. 37. SHARESemantic Health And Research Environment<br />SPARQL enhanced by SADI<br />
  38. 38. A Novel SPARQL Query Engine<br />Overcomes some of the limitations of traditional SPARQL query-handlers<br />
  39. 39. A Novel SPARQL Query Engine<br />Overcomes some of the limitations of traditional SPARQL query-handlers<br />…and more…<br />
  40. 40. A Novel SPARQL Query Engine<br />Overcomes some of the limitations of traditional SPARQL query-handlers<br />…and more…<br />MUCH more!!<br />
  41. 41. What pathways does UniProt protein P47989 belong to?<br />PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#><br />PREFIX ont: <http://ontology.dumontierlab.com/><br />PREFIX uniprot: <http://lsrn.org/UniProt:><br />SELECT ?gene ?pathway <br />WHERE { <br /> uniprot:P47989 pred:isEncodedBy ?gene . <br /> ?gene ont:isParticipantIn ?pathway . <br />}<br />
  42. 42. What pathways does UniProt protein P47989 belong to?<br />PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#><br />PREFIX ont: <http://ontology.dumontierlab.com/><br />PREFIX uniprot: <http://lsrn.org/UniProt:><br />SELECT ?gene ?pathway <br />WHERE { <br /> uniprot:P47989 pred:isEncodedBy ?gene . <br /> ?gene ont:isParticipantIn ?pathway . <br />}<br />
  43. 43. What pathways does UniProt protein P47989 belong to?<br />PREFIX pred: <http://sadiframework.org/ontologies/predicates.owl#><br />PREFIX ont: <http://ontology.dumontierlab.com/><br />PREFIX uniprot: <http://lsrn.org/UniProt:><br />SELECT ?gene ?pathway <br />WHERE { <br />uniprot:P47989pred:isEncodedBy ?gene . <br /> ?geneont:isParticipantIn ?pathway . <br />}<br />Note that there is no “From” clause… I have neglected to tell the system where to look for the answer, I am simply asking my question<br />
  44. 44. Now stick that query into SHARE<br />
  45. 45.
  46. 46.
  47. 47. Recapwhat we just saw<br />A standard SPARQL query was entered into SHARE, a SADI-aware query engine<br />
  48. 48. Recapwhat we just saw<br />The query was interpreted to extract the individual data/relationships being requested <br />(and any component/sub-properties, as we shall see later!)<br />
  49. 49. Recapwhat we just saw<br />The “triple-patterns” required to answer the query are passed to SADI for Web Service discovery<br />
  50. 50. Recapwhat we just saw<br />Services capable of generating those triple-patterns are automatically executed, the triples are stored, and the query is resolved.<br />
  51. 51. Recapwhat we just saw<br />We posed, and answered a ~complex database query <br />WITHOUT A DATABASE<br />(in fact, the data didn’t even have to exist...)<br />
  52. 52. Holy Grail Demo #1<br />Align the promoters of all serine threonine kinases involved exclusively in the regulation of cell sorting during wound healing in blood vessels.<br />Retrieve and align 2000nt 5' from every serine/threonine kinase in Mus musculus expressed exclusively in the tunica [I | M |A] whose expression increases 5X or more within 5 hours of wounding but is not activated during the normal development of blood vessels, and is <40% homologous in the active site to kinases known to be involved in cell-cycle regulation in any other species.<br />
  53. 53. Holy Grail Demo #2<br />
  54. 54. Show me the latest Blood Urea Nitrogen and Creatinine levelsof patients who appear to be rejecting their transplants<br />PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> <br />PREFIX patient: <http://sadiframework.org/ontologies/patients.owl#> <br />PREFIX l: <http://sadiframework.org/ontologies/predicates.owl#> <br />SELECT ?patient ?bun ?creat<br />FROM <http://sadiframework.org/ontologies/patients.rdf><br />WHERE {<br /> ?patientrdf:typepatient:LikelyRejecter .<br /> ?patient l:latestBUN ?bun . <br /> ?patient l:latestCreatinine ?creat . <br />}<br />
  55. 55. Likely Rejecter:<br />A patient who has creatinine levelsthat are increasing over time<br />- - Wilkinson MD<br />
  56. 56. Likely Rejecter:<br />…but there is no “likely rejecter” column or table in our database… only blood chemistry measurementsat various time-points<br />
  57. 57. ?<br />
  58. 58. The definition of a LikelyRejecter is encoded in a machine-readable document written in the OWL language (“Ontology”)<br />“the regression line over creatinine measurements should have an increasing slope”<br />
  59. 59. The machine continues to burrow down through the definition and discovers that regression lines have things like slopes and intercepts, etc…<br />
  60. 60. Then… <br />Two magical events occur…<br />
  61. 61. The machine figures out<br />by itselfthe need to do a Linear Regression analysisin order to answer your question<br />
  62. 62. The machine figures out<br />by itselfhow and wherethat analysiscan be doneand does it automatically!<br />
  63. 63. http://www.impactlab.net/2009/03/22/improve-your-brain-power/<br />
  64. 64. The SHARE system utilizes SADI to discover analytical services on the Web that do linear regression analysis<br />
  65. 65. VOILA!<br />
  66. 66. How do we do that?!?<br />We let the data describe itself!<br />This is a different frommost of the bioinformatics world,where the person giving you the data also tells you how to interpret it <br />
  67. 67. Data exhibits “late binding”<br />
  68. 68.
  69. 69. Late binding:“purpose and meaning”of the data isnot determined untilthe moment it is required<br />
  70. 70. Benefit<br />of late binding<br />Data is amenable to<br />constant re-interpretation<br />
  71. 71. Example?<br />Blood Creatinine measurements<br />were not dictated to be (only)<br />Blood Creatinine measurements!<br />
  72. 72. Example?<br />The data had the ‘qualities/properties’ that<br />allowed the machine to infer<br />that they were Blood Creatinine measurements <br />
  73. 73. Example?<br />But the data also had the ‘qualities/properties’ that <br />allowed them to be interpreted as <br />X/Y coordinate data by another Service<br />
  74. 74. http://www.flickr.com/people/faernworks/<br />
  75. 75. Holy Grail Demo #2<br />Align the promoters of all serine threonine kinases involved exclusively in the regulation of cell sorting during wound healing in blood vessels.<br />Retrieve and align 2000nt 5' from every serine/threonine kinase in Mus musculus expressed exclusively in the tunica [I | M |A] whose expression increases 5X or more within 5 hours of wounding but is not activated during the normal development of blood vessels, and is <40% homologous in the active site to kinases known to be involved in cell-cycle regulation in any other species.<br />
  76. 76. The Holy Grail may not yet be in-handbut we can at least see it from here!So… now what?<br />
  77. 77. Mark’s Manifesto<br />What is my next “Holy Grail”?<br />
  78. 78. Science<br />Support for the in silico<br />Scientific Method<br />
  79. 79.
  80. 80. The Scientific Method<br />Discourse: What do you believe? What do I believe?<br />Disagreement: You’re wrong! And I’m gonna prove it!<br />Clarity: This is the experiment I am going to do<br />Reproducibility: This is how I did it (“provenance”)<br />Clarity: This is my new hypothesis<br />
  81. 81. The Scientific Method<br />Discourse: What do you believe? What do I believe?<br />Disagreement: You’re wrong! And I’m gonna prove it!<br />Clarity: This is the experiment I am going to do<br />Reproducibility: This is how I did it (“provenance”)<br />Clarity: This is my new hypothesis<br />Workflows <br /> (e.g. myExperiment) <br />
  82. 82. Another Brief Digression…<br />
  83. 83. “Facebook” for Scientists<br />http://myexperiment.org<br />
  84. 84. An exciting evolution in the way Researchers express and share their in silico “Materials and Methods”<br />Through things called ‘Workflows’<br />
  85. 85.
  86. 86. Workflows are explicit representationsof the method by which an analysis was doneand which resources are used to do it<br />
  87. 87. Workflows can be very simple…<br /> “Blast this sequence”<br />
  88. 88. Or not...<br />This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) <br />Also returned by this workflow are a list of the top differentially expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed changes in the microarray data.<br />
  89. 89. Why bother?<br />
  90. 90. Taverna<br />A workbench for designing and executingScientific Workflows<br />
  91. 91.
  92. 92. Load-up your data and press “play”!<br />…Then go home for the weekend! You are just one click away from your M.Sc.!!<br />
  93. 93. By the by…<br />The SHARE application automatically creates a Workflow and then automatically runs it.This is where the data comes from to answer the queries… Workflows are a Good Thing™ <br />
  94. 94. Detour EndsPlease resume speed<br />
  95. 95. WORKFLOWS<br />
  96. 96.
  97. 97. At the moment <br />the Semantic Web in Healthcare and Life Sciencesaddresses these issues by attempting to create “consensus”<br />
  98. 98. Large, centralized ontologies <br />(e.g. the Gene Ontology)<br />that claim to represent community agreement about “biological reality”<br />
  99. 99. …is that Science?<br />
  100. 100.
  101. 101.
  102. 102.
  103. 103.
  104. 104. To restore the “traditions of Science” to in silico science<br />The Semantic Web needs to encourage/facilitate personal opinion and debate<br />
  105. 105. What has this got to do with SADI and SHARE?<br />
  106. 106. PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> <br />PREFIX patient: <http://sadiframework.org/ontologies/patients.owl#> <br />PREFIX l: <http://sadiframework.org/ontologies/predicates.owl#> <br />SELECT ?patient ?bun ?creat<br />FROM <http://sadiframework.org/ontologies/patients.rdf><br />WHERE {<br /> ?patientrdf:typepatient:LikelyRejecter .<br /> ?patient l:latestBUN ?bun . <br /> ?patient l:latestCreatinine ?creat . <br />}<br />
  107. 107. Likely Rejecter<br />
  108. 108. I created a small ontology describing my definition ofa Likely Rejecter<br />
  109. 109. … it was MY ontology!<br />
  110. 110. I can re-use it<br />
  111. 111. I can modify it as I change myworld-view<br />
  112. 112. I can publish it for others to use<br />
  113. 113. Others can modify it and/or compare it to THEIR world-view<br />
  114. 114. Sharing my ontology gives opportunities for “micro-attribution”“Credit” to me is automatic when someone uses my ontology in their ontology/query<br />
  115. 115. Using SADI and SHAREmypersonal world-view isexplicitlyexpressedand can bedynamically evaluated againstglobal data and knowledge<br />
  116. 116. http://www.dailymail.co.uk/femail/article-488234/Friends-dignity-self-respect---weight-wasnt-I-lost-slimming-club.html<br />
  117. 117. …but there’s more…<br />
  118. 118. “Likely Rejecter”<br />
  119. 119. I made that up! It came out of my head!<br />
  120. 120. What’s another word for a world-view that you make-up?<br />Hypothesis<br />
  121. 121. The “Likely Rejecter” OWL Class<br />is an explicitly-expressed hypothesis;<br />Members of that class may or may not exist!<br />
  122. 122.
  123. 123.
  124. 124. Ontologically-expressed Hypotheses drive the discovery, assembly, and analysis of data capable of evaluating their validity<br />Hypothesis<br />Ischemia<br />SADI<br />+ <br />SHARE<br />Hypertension<br />Blood Pressure<br />Analytical Algorithm<br />Database 1<br />Database 2<br />
  125. 125. Join us!<br />SADI and CardioSHARE are Open-Source projects<br />Come join us – we’re having a lot of fun!!<br />http://sadiframework.org<br />
  126. 126. Credits<br />Benjamin VanderValk(SHARE & SADI)<br />Luke McCarthy (SADI, SHARE, Taverna, CardioSHARE)<br />SoroushSamadian(CardioSHARE)<br />David Withers(Taverna)<br />Edward Kawas(SADI Service auto-generator)<br />
  127. 127. U of New Brunswick<br />Dr. Chris BakerAlexandreRiazanov<br />Carleton University<br />Dr. Michel Dumontier<br /> Marc-Alexandre Nolin<br /> Leonid Chepelev<br /> Steve Etlinger<br />NichaellaKieth<br /> Jose Cruz<br />
  128. 128. Microsoft Research<br />
  129. 129. Credits<br />Benjamin VanderValk (SADI & CardioSHARE)<br />Luke McCarthy (SADI & CardioSHARE)<br />SoroushSamadian (CardioSHARE)<br />IO Informatics (Knowledge Explorer API)<br />Microsoft Research<br /> Fin<br />This presentation available on SlideShare: keywords ‘wilkinson’ ‘iCAPTURE’ ‘HLI’<br />
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