A talk given at the Unilever Centre for Molecular Informatics, Chemistry, Cambridge University on 12 May 2009. The talk covers issues to do with capturing research processes and objects taking inspiration from linked open data and distributed version control systems. Live blogged by Nico Adams at http://wwmm.ch.cam.ac.uk/blogs/adams/?p=249

2. Richard Grant Mat Todd Hide Plausible Accuracy
Pedro Beltrao
John Branwen
Rich Apodaca
Dupuis Neil Saunders Steve Wilson Simon Coles Noel
Tony Hey Pawel SzcsesnyRichard Akerman Gorelick
Dave de Roure
Jon Tim O’Reilly Victoria Stodden Jeremy Frey
ISIS LSS Group
Udell Jean-Claude Bradley
Jeremiah Faith Martyn Bull
Michael Barton John Cumbers
Clay Shirky
Bora David Crotty Helen
Egon Willighagen
Brian Kelly Tony Williams Tim O’Reilly Berman
Zivkovic Maxine Clarke Andrew
Michael Nielsen
Frank Mitch Martin Fenner Milsted
Jenny Rohn
NormanWaldrop Wilson
Greg
Yaroslav Nikolaev Iain Emsley Rafael Sidi Lee Smolin
Lorie LeJeune JonathanHooker Bill
Timo Hannay
Gray
Ken Shankland Paulo Nuin
Deepak Singh Shirley Wu Liz Lyons PLoS
STFC
Friendfeed Peter Binfield Benjamin Good Dorothea Salo
Peter Murray-Rust Richard Akerman
Jen Dodd
Chad Orzel Lakshmi Shastry ISIS Computing Group
Jon Eisen Jenny Hale
ciFoo 2008 Flanagan
Bill Matt Wood
Michael Eisen
Jon Tansley
Victor HenningGoogle Björn Brembs
campers
Rufus Pollock
John TIM HUBBARD
Gavin Bell
Andy Powell Harry Collins
Wilbanks
Mike Ellis Garret Lisi
DUNCAN HULL
Euan Adie Peter Suber
Gavin Baker
The BioGang
Sabine Hossenfelder
Paul Walk
Flickr Kevin Kelly
Kaitlin Thaney Richard Curry Atilla Csordas Ian Mulvaney

3. Capturing Process
In silico, in the lab, and all the messy in betweens

4. Laboratory Computational
procedures procedures
Procedure Experiment Analysis
Data Data
Material(s) Sample(s)
Physical objects Digital objects

5. http://www.flickr.com/photos/halfchinese/113968722 CC-BY

6. Data is dynamic...
http://www.flickr.com/photos/idletype/282855293/ CC-BY

7. Inspiration from coding best practice
Repositories for storage/backup
Strong record of who and when
Roll-back, diffs, and reversion
Testing as part of the process
Scripting for solid replication

8. Working independently...
http://www.flickr.com/photos/tswicegood/3233621766/ CC-BY-SA

9. ...data integration
http://www.flickr.com/photos/tbisaacs/3087193160/ CC-BY

10. ...but commits are freetext

11. DVCS systems can provide who, when,
what and differences between versions
But it doesn’t provide the relationships
between objects...

12. Have a good provenance trail...
http://www.flickr.com/photos/a4gpa/195354385 CC-BY-SA

13. ...but not a good map of how
that relates to everything else
http://www.flickr.com/photos/normanbleventhalmapcenter/2674855383 CC-BY

14. If we have the map...
...if we capture the connections

15. http://is.gd/thVr

16. ...and on to a semantic web of data

17. ...but what about in here?
http://www.flickr.com/photos/mararie/2151361243 CC-BY-SA

18. Lab book as a journal...
http://www.flickr.com/photos/nbachiyski/2186228572 CC-BY

19. Blog as journal...

20. Description, date
categorisation,
objects, identity,
accessibility...
...not of much
interest to most
people

21. http://biolab.isis.rl.ac.uk/projects/blog/

24. http://is.gd/thMB

25. http://is.gd/thMB

26. Laboratory Computational
procedures procedures
Procedure Experiment Analysis
Data Data
Material(s) Sample(s)
Physical objects Digital objects

27. A web of objects...

28. A web of objects...

29. A web of objects...
...and the process
that connects them

30. ...but still not semantic

31. Tagging goes some way...
...but how to enforce tagging?

32. Templates create a virtuous circle
[table]
[row]
Lane[col]Sample[col]ul
[/row]
…
[row]
4[col][[Dna:%]][col][[box]]
[/row]
…
[/table]
[[Section>Procedure]]
[[Procedure_Type>electrophoresis_agarose]]
[[Sandpit_group>DrexelDemo]]

33. Templates create a virtuous circle
[table]
[row]
Lane[col]Sample[col]ul
[/row]
…
[row]
4[col][[Dna:%]][col][[box]]
[/row]
…
[/table]
[[Section>Procedure]]
[[Procedure_Type>electrophoresis_agarose]]
[[Sandpit_group>DrexelDemo]]

34. Templates create a virtuous circle
[table]
[row]
Lane[col]Sample[col]ul
[/row]
…
[row]
4[col][[Dna:%]][col][[box]]
[/row]
…
[/table]
[[Section>Procedure]]
[[Procedure_Type>electrophoresis_agarose]]
[[Sandpit_group>DrexelDemo]]

35. Self assembling ontology?
Sequence ontology:
SO:0000696 “oligo”
SO:0000155 “plasmid”
...but...
SO:0000006 “PCR product”
or
SO:0000412 “rest. fragment”?
Mixing up of process of production and material type?

36. We need a robust ontology or
controlled vocabulary for experiments...
...but with that in hand
http://www.flickr.com/photos/peterkaminski/5444915 CC-BY

37. We can build a semantic web of objects
...and the processes that connect them

38. Linked open data and
linked open objects
http://is.gd/thVr

39. Building for the future?
http://www.flickr.com/photos/blahflowers/1382374610 CC-BY-SA

40. Capture it at source...
...in context
http://flickr.com/photos/jason_burmeister/2053139930 CC-BY

41. Capture as much as possible automatically
Slide adapted from original by Simon Coles

42. In silico capture the
process step by step...
http://www.flickr.com/photos/stevoarnold/2787234769 CC-BY

43. In silico capture the
process step by step...
...one way or another the
semantics can be baked in
http://www.flickr.com/photos/stevoarnold/2787234769 CC-BY

44. In the lab capture each object
as it is created...

45. In the lab capture each object
as it is created...
...and capture the plan and
track execution step by step

46. Plan
=
Template
=
Minimal Information Foo
=
Semantics

47. Data repositories...
...as easy to use as Flickr

51. More natural interfaces...
http://www.flickr.com/photos/bekathwia/2910518374 CC-BY-SA

52. More natural interfaces...
...to capture and communicate
http://www.flickr.com/photos/bekathwia/2910518374 CC-BY-SA

53. ...Pages from a project need
to be linked in a 3D web of
relevance...I want to be able
to annotate a...collaborator's
work by drawing on it...as I
would write on [their]
whiteboard...
Mat Todd
http://is.gd/yVQK
http://www.flickr.com/photos/andypowe11/2938538086 CC-BY

54. But who (and what) can you trust?
http://www.flickr.com/photos/joi/2941559903 CC-BY

55. We trust people...
...not objects

56. A semantic social web
of objects (and data,
and process and...)

57. (Some of) the
people I trust...
...in dierent
ways and for
dierent things

58. http://friendfeed.com

59. Code
Data
Sample
Process
http://friendfeed.com/lists/isisbiolab

60. Data finds the data,
then people find people.
Jeff Jonas/Jon Udell via Deepak Singh

61. It’s the objects that are the
centre of the social interaction
and not the people

68. But that can only work
if these objects are...

69. http://flickr.com/photos/virtualsugar/316200555/ CC-BY

70. Connected research
changes the playing field

71. Connected research
changes the playing field
...availability of
resources key

72. We need to capture objects
as they are created...

73. We need to capture objects
as they are created...
...and to capture
their relationships

74. The rest we can build
bit by bit as we go

75. Communicate first,
standardize second.
Jean-Claude Bradley