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.

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/107787363

...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 chemistry
http://mytea.org.uk/

But not molecular biology

General
MyTea
Specific
Unstructured Structured

General
?
MyTea
Specific
Unstructured Structured

General
Blogs
?
MyTea
Specific
Unstructured Structured

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

Yes to start with...

But then something
interesting happened...

Templates Metadata

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

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

Natural user interaction
Easy user interaction with
web services and databases
Per user, per experiment, per
group storage of information

Problems...

The client.
User understanding.

Conclusions.

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

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