Capturing Process: Challenges and opportunities

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? 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

http://scienceroll.com	32
http://cameronneylon.net	27
http://static.slidesharecdn.com	17
https://0-wave-opensocial.googleusercontent.com	1
http://127.0.0.1:8795	1
http://www.slideshare.net	1

Capturing Process: Challenges and opportunities

by Cameron Neylon

Accessibility

Categories

Upload Details

Usage Rights

6 Embeds 79

Statistics