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 ...

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.

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Capturing Process: Challenges and opportunities Capturing Process: Challenges and opportunities Presentation Transcript

  • Capturing Process: Promise and Challenges.
  • http://www.flickr.com/photos/davidcjones/1422043515
  • The first step... http://www.flickr.com/photos/laprimadonna/3611292727/ View slide
  • ...is to admit we have http://www.flickr.com/photos/schnurrbart/43568532/ CC-BY-SA View slide
  • 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