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.

Education

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
1982 1986 1990 1994 1998 2002 2006

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.

...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..

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 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? That’s
really exciting!

1. Capture
2. Communicate
Communicate

Process

...but useful sharing is
harder than publishing
http://www.ﬂickr.com/photos/missrogue/107787363

...need agreed structure

http://www.ﬂickr.com/photos/sﬂlaw/222795669

Machines need structure

http://www.ﬂickr.com/photos/yeowatzup/2463225297

MyTea project:
A fully semantic
laboratory record
for chemistry
http://mytea.org.uk/

General

MyTea
Speciﬁc

Unstructured Structured

General
Blogs

?

MyTea
Speciﬁc

Unstructured Structured

A recipe for chaos?

http://www.ﬂickr.com/photos/benuski/3452291541

But then something
interesting happened...

Self assembling ontology?
Sequence ontology:
SO:0000696 “oligo”
SO:0000155 “plasmid”

...but...

SO:0000006 “PCR product”
or
SO:0000412 “rest. fragment”?

Capture first...

http://www.ﬂickr.com/photos/furtwangl/3851841424

Dionaea muscipula Musca domestica
chomped on

...then add structure

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

Euan Adie’s Igor Robot
User conversation with
services

ChemSpidey
Linking identifiers to
databases

Workflows
Robots can interact with
each other easily

Natural user interaction

Easy user interaction with
web services and databases

Per user, per experiment, per
group storage of information

...tools to capture structure

...as we tell the story

Less of this...

http://www.ﬂickr.com/photos/tranchis/3708549622

...more of this

http://www.ﬂickr.com/photos/chadmiller/2740551034

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Capturing Process: Challenges and opportunities

1. Capturing Process: Promise and Challenges.

2. http://www.ﬂickr.com/photos/davidcjones/1422043515

3. The first step... http://www.ﬂickr.com/photos/laprimadonna/3611292727/

4. ...is to admit we have http://www.ﬂickr.com/photos/schnurrbart/43568532/ CC-BY-SA

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. Average Capacity of Human Scientist 5.00 3.75 2.50 1.25 0 1982 1986 1990 1994 1998 2002 2006

7. The human scientist (that’s us) Does. Not. Scale.

8. The web scales

9. I need help!

10. ...RDF...XML.... JSON...Rest...Atom Pub...RSS..SOAP... Java...xmlns

11. ?

12. ...£££££...

13. ...computers...don’t I have a nephew who can do that?

14. OBI...Mibbi... FuGE...OBO...RDF ...standards...XML.. ...standards..

15. ...wibble...

16. You’re not a proper scientist unless you do it our way...

17. http://www.ﬂickr.com/photos/tranchis/3708549622

18. I want to record the work from my group so I can ﬁnd it again.

19. I want to be able to communicate knowledge clearly

20. I want to record the work from my group so I can ﬁnd it again.

21. ...£££££...

22. I want to be able to take your data and do cool stuff with it

23. You mean other people might use our work? Can’t be having that!

24. You mean other people might use our work? Can’t be having that!

25. You mean other people might use our work? That’s really exciting!

26. 1. Capture 2. Communicate Communicate Process

27. Capture research objects...

28. ...publish to the web...

29. ...in most appropriate form

30. ...but useful sharing is harder than publishing http://www.ﬂickr.com/photos/missrogue/107787363

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

32. Machines need structure http://www.ﬂickr.com/photos/yeowatzup/2463225297

33. ....humans tell stories

34. Capture research objects

35. Publish

36. Capture structure through story telling

37. A story.

38. MyTea project: A fully semantic laboratory record for chemistry http://mytea.org.uk/

39. But not molecular biology

40. General MyTea Speciﬁc Unstructured Structured

41. General ? MyTea Speciﬁc Unstructured Structured

42. General Blogs ? MyTea Speciﬁc Unstructured Structured

43. A recipe for chaos? http://www.ﬂickr.com/photos/benuski/3452291541

44. Yes to start with...

45. But then something interesting happened...

46. Templates Metadata

47. Self assembling ontology? Sequence ontology: SO:0000696 “oligo” SO:0000155 “plasmid” ...but... SO:0000006 “PCR product” or SO:0000412 “rest. fragment”?

48. Capture first... http://www.ﬂickr.com/photos/furtwangl/3851841424

49. Dionaea muscipula Musca domestica chomped on ...then add structure

50. Map our process onto agreed vocabularies

51. ...when we tell the story http://www.ﬂickr.com/photos/tnarik/366393127

52. Tools that capture structure as we choose the pieces for our narrative

53. Tools that exploit structure where it already exists

54. Instruments as bloggers...

55. Tools to tell stories?

56. Tools to wire up the objects?

57.

58.

59. Tools to connect to services?