Capturing Process: Challenges and opportunities

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A talk given at the Computer Science Department, Newcastle University. The talk focusses on the problems involved in capturing information from experimental science and proposes the development of tools that capture data and metadata through the experimentalist constructing a narrative.

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Capturing Process: Challenges and opportunities

  1. 1. Capturing Process: Promise and Challenges.
  2. 2. http://www.flickr.com/photos/davidcjones/1422043515
  3. 3. The first step... http://www.flickr.com/photos/laprimadonna/3611292727/
  4. 4. ...is to admit we have http://www.flickr.com/photos/schnurrbart/43568532/ CC-BY-SA
  5. 5. Submissions to Genbank 100,000,000,000 75,000,000,000 50,000,000,000 25,000,000,000 0 1982 1986 1990 1994 1998 2002 2006
  6. 6. Average Capacity of Human Scientist 5.00 3.75 2.50 1.25 0 1982 1986 1990 1994 1998 2002 2006
  7. 7. The human scientist (that’s us) Does. Not. Scale.
  8. 8. The web scales
  9. 9. I need help!
  10. 10. ...RDF...XML.... JSON...Rest...Atom Pub...RSS..SOAP... Java...xmlns
  11. 11. ?
  12. 12. ...£££££...
  13. 13. ...computers...don’t I have a nephew who can do that?
  14. 14. OBI...Mibbi... FuGE...OBO...RDF ...standards...XML.. ...standards..
  15. 15. ...wibble...
  16. 16. You’re not a proper scientist unless you do it our way...
  17. 17. http://www.flickr.com/photos/tranchis/3708549622
  18. 18. I want to record the work from my group so I can find it again.
  19. 19. I want to be able to communicate knowledge clearly
  20. 20. I want to record the work from my group so I can find it again.
  21. 21. ...£££££...
  22. 22. I want to be able to take your data and do cool stuff with it
  23. 23. You mean other people might use our work? Can’t be having that!
  24. 24. You mean other people might use our work? Can’t be having that!
  25. 25. You mean other people might use our work? That’s really exciting!
  26. 26. 1. Capture 2. Communicate Communicate Process
  27. 27. Capture research objects...
  28. 28. ...publish to the web...
  29. 29. ...in most appropriate form
  30. 30. ...but useful sharing is harder than publishing http://www.flickr.com/photos/missrogue/107787363
  31. 31. ...need agreed structure http://www.flickr.com/photos/sfllaw/222795669
  32. 32. Machines need structure http://www.flickr.com/photos/yeowatzup/2463225297
  33. 33. ....humans tell stories
  34. 34. Capture research objects
  35. 35. Publish
  36. 36. Capture structure through story telling
  37. 37. A story.
  38. 38. MyTea project: A fully semantic laboratory record for chemistry http://mytea.org.uk/
  39. 39. But not molecular biology
  40. 40. General MyTea Specific Unstructured Structured
  41. 41. General ? MyTea Specific Unstructured Structured
  42. 42. General Blogs ? MyTea Specific Unstructured Structured
  43. 43. A recipe for chaos? http://www.flickr.com/photos/benuski/3452291541
  44. 44. Yes to start with...
  45. 45. But then something interesting happened...
  46. 46. Templates Metadata
  47. 47. Self assembling ontology? Sequence ontology: SO:0000696 “oligo” SO:0000155 “plasmid” ...but... SO:0000006 “PCR product” or SO:0000412 “rest. fragment”?
  48. 48. Capture first... http://www.flickr.com/photos/furtwangl/3851841424
  49. 49. Dionaea muscipula Musca domestica chomped on ...then add structure
  50. 50. Map our process onto agreed vocabularies
  51. 51. ...when we tell the story http://www.flickr.com/photos/tnarik/366393127
  52. 52. Tools that capture structure as we choose the pieces for our narrative
  53. 53. Tools that exploit structure where it already exists
  54. 54. Instruments as bloggers...
  55. 55. Tools to tell stories?
  56. 56. Tools to wire up the objects?
  57. 57. Tools to connect to services?
  58. 58. Google Wave as a Solution
  59. 59. Euan Adie’s Igor Robot User conversation with services
  60. 60. ChemSpidey Linking identifiers to databases
  61. 61. Workflows Robots can interact with each other easily
  62. 62. The potential
  63. 63. Natural user interaction Easy user interaction with web services and databases Per user, per experiment, per group storage of information
  64. 64. Problems...
  65. 65. The client. User understanding.
  66. 66. Conclusions.
  67. 67. Average Capacity of Human Scientist 5.00 3.75 2.50 1.25 0 1982 1986 1990 1994 1998 2002 2006
  68. 68. I need help!
  69. 69. Machines need structure http://www.flickr.com/photos/yeowatzup/2463225297
  70. 70. ....humans tell stories
  71. 71. Tools to capture...
  72. 72. ...tools and services to publish...
  73. 73. ...tools to capture structure ...as we tell the story
  74. 74. Capturing.
  75. 75. Communication.
  76. 76. Two different things.
  77. 77. Less of this... http://www.flickr.com/photos/tranchis/3708549622
  78. 78. ...more of this http://www.flickr.com/photos/chadmiller/2740551034

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