Capturing Process:
   Promise and Challenges.
http://www.flickr.com/photos/davidcjones/1422043515
The first step...




http://www.flickr.com/photos/laprimadonna/3611292727/
...is to admit we have




http://www.flickr.com/photos/schnurrbart/43568532/ CC-BY-SA
Submissions to Genbank
100,000,000,000


 75,000,000,000


 50,000,000,000


 25,000,000,000


             0
            ...
Average Capacity of Human Scientist
5.00


3.75


2.50


1.25


  0
  1982     1986   1990   1994   1998   2002   2006
The human scientist
     (that’s us)
 Does. Not. Scale.
The web scales
I need help!
...RDF...XML....
JSON...Rest...Atom
Pub...RSS..SOAP...
    Java...xmlns
?
...£££££...
...computers...don’t
   I have a nephew
  who can do that?
OBI...Mibbi...
 FuGE...OBO...RDF
...standards...XML..
    ...standards..
...wibble...
You’re not a proper
scientist unless you
  do it our way...
http://www.flickr.com/photos/tranchis/3708549622
I want to record
the work from my
group so I can find
     it again.
I want to be able
 to communicate
knowledge clearly
I want to record
the work from my
group so I can find
     it again.
...£££££...
I want to be able to
take your data and
do cool stuff with it
You mean other
 people might use
our work? Can’t be
    having that!
You mean other
 people might use
our work? Can’t be
    having that!
You mean other
people might use
our work? That’s
  really exciting!
1. Capture
              2. Communicate
Communicate




                    Process
Capture research objects...
...publish to the web...
...in most appropriate form
...but useful sharing is
                              harder than publishing
http://www.flickr.com/photos/missrogue/107787...
...need agreed structure




http://www.flickr.com/photos/sfllaw/222795669
Machines need structure




http://www.flickr.com/photos/yeowatzup/2463225297
....humans tell stories
Capture research objects
Publish
Capture structure
through story telling
A story.
MyTea project:
                       A fully semantic
                       laboratory record
                       for...
But not molecular biology
General




                    MyTea
Specific

     Unstructured   Structured
General


                    ?

                        MyTea
Specific

     Unstructured       Structured
General
            Blogs


                    ?

                        MyTea
Specific

     Unstructured       Structur...
A recipe for chaos?




http://www.flickr.com/photos/benuski/3452291541
Yes to start with...
But then something
interesting happened...
Self assembling ontology?
               Sequence ontology:
               SO:0000696 “oligo”
               SO:0000155 “p...
Capture first...




http://www.flickr.com/photos/furtwangl/3851841424
Dionaea muscipula                 Musca domestica
                     chomped on




                    ...then add stru...
Map our process onto
 agreed vocabularies
...when we tell the story




http://www.flickr.com/photos/tnarik/366393127
Tools that capture
  structure as we choose
the pieces for our narrative
Tools that exploit structure
  where it already exists
Instruments as bloggers...
Tools to tell stories?
Tools to wire up the objects?
Tools to connect to services?
Google Wave as a Solution
Euan Adie’s Igor Robot
User conversation with
       services
ChemSpidey
Linking identifiers to
     databases
Workflows
Robots can interact with
   each other easily
The potential
Problems...
Conclusions.
I need help!
Machines need structure




http://www.flickr.com/photos/yeowatzup/2463225297
....humans tell stories
Tools to capture...
...tools and services to publish...
...tools to capture structure




             ...as we tell the story
Capturing.
Communication.
Two different things.
Less of this...




http://www.flickr.com/photos/tranchis/3708549622
...more of this

http://www.flickr.com/photos/chadmiller/2740551034
Capturing Process: Challenges and opportunities
Capturing Process: Challenges and opportunities
Capturing Process: Challenges and opportunities
Capturing Process: Challenges and opportunities
Capturing Process: Challenges and opportunities
Capturing Process: Challenges and opportunities
Capturing Process: Challenges and opportunities
Capturing Process: Challenges and opportunities
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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.

Published in: Education

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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