Inside Laboratory 2.0
Jeremy Frey
University of Southampton
The impact and influence of Web 2.0-based
Services on e-Research
“The internet wasn't created for mockery!
It was created so scientists from different
universities could share datasets....”
Simpson, H. The Simpsons (2005), Eds. Groening, M., Brooks, J.L.
& Simon, S., Series 16, Episode 8, Original air date (US) 06-Feb2005.
http://www.tvtome.com/tvtome/servlet/GuidePageServlet/showi
d-146/epid-346864/
In a move to preserve civilization for
future generations, the world’s leaders
announced Monday their decision to
have the accumulated knowledge of all
areas of human endeavor written down.
“Once this information is transferred to a
permanent record on the printed page,”
explained British Prime Minister John
Major via satellite, “the children of
tomorrow will be able to access our
knowledge by visually scanning or
‘reading’ the information similar to the
way you see me speaking on your
television.”
Data Generation in Chemistry
Characterisation
Synthesis
Data Deluge
40 years ago a PhD student would
determine about 3 crystal
structures for their thesis – this can
now be easily achieved in a day
0.5 million
35 million
2.5 million
‘Few
thousand’
The primary cause is the current data publication process,
which is tied to journal articles and peer review
Data Publication &
Information Loss
Spectroscopic analysis is often performed to
ensure a reaction is proceeding according to
plan – as a result <5% are published (via a
process with heavy information loss)
http://www.theonion.com/content/node/28104
The Solution
Intellect &
Interpretation
(Journal article,
report, etc)
Underlying data
(Institutional
data repository)
Core of Self describing data
• Store of data that can
be viewed and
manipulated in different
ways
• User interfaces to suite
user and occasion
He is charged with expressing contempt
for meta-data
Late 20th Century Labs
Experience – Grey Literature
People
Equipment
Lab Records
Environment
Literature
Computation
Late 20th Century Labs
Experience – Grey Literature
Lab Records
Computer
Computer
People
Equipment
Environment
Computation
Computer
Computer
Computer
Computer
Computer
Literature
Experience – Grey Literature
Lab Records
Computer
People
Computer
Computer
Computer
Environment
Computer
Computation
ELN
Blog
MyExpt
Equipment
21th Century Labs
Computer
Computer
Literature
Blog
Wiki
Repositories
User interfaces
Time
Line
Planning
Information
Data +
Metadata
Virtual World
Social Networks
Google Wave
“MyExperiment”
Faraday’s laboratory
notebooks are also
remarkable in the amount of
detail that they give about
the design and setting up of
experiments, interspersed
with comments about their
outcome and thoughts of a
more philosophical kind. All
are couched in plain
language, with many vivid
phrases of delightful
spontaneity….
Peter Day, ‘The Philosopher’s
Tree: A Selection of Michael
Faraday’s Writings’
Observations are never
collected on note pads,
filter paper or other
temporary paper for
later transfer into a
notebook
If you are caught using the
“scrap of paper” technique,
your improperly recorded data
may be confiscated by your TA
Literature
Formal Literature
Grey Literature
Databases
Repositories
Lab Blog
ELN
Experiments
Experiments
Repositories
Experiments
Middleware
• Middleware is the connecting software between separated
components
• Message brokering system used
• Increases scalability and interoperability
• Without middleware
• With middleware
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meta
Analysis & Discussion: Blogging
Experiments
A repository…
• Allows one to put, store and get
• Provides search and browse
• DOES NOT provide presentation
and discussion functions essential to
working up a scientific study
• ‘Geographically distributed
collaborative research’
• Open or private
• A useful approach for sharing
‘failed’ experiments?
http://chemtools.chem.soton.ac.uk/projects/blog/
Blogging Innovations
Machines
Sensors
Tools
Time Line View
Journal publication
Test Data
Management
Grant Applications
Analysis
/
Conference reports
RESULTS!
Online
blog3 Stack
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User Directory
Cell
Blog Management
Simple Experiment Ontology
Link with OREChem
Validation
• Increasing the value of data
• How to bring all the necessary
information together to enable
appropriate validation
• Increasingly difficult &
expensive to achieve
Need provenance and context otherwise just
a collection of items
oreChem – The Chemical Semantic Web
•
•
•
•
•
•
•
At-source capture of chemistry data
Chemical structure search
Compound object authoring
Retrospective harvesting of chemistry data
Reuse through common ORE data model
Semantic authoring
Virtualized triple storage
•
•
•
•
•
•
University of Cambridge
Cornell University
Indiana University
Penn State University
University of Queensland
University of Southampton
Mash-up
(reuse)
Semantic
Graph
(storage)
experiments
text
measurements
Data
(capture)
documents
data
scientists
molecules
data
molecules
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The Circle of Attribution
Store Link
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Confusion of Digital Reality
http://www.theonion.com/content/node/29147
Awareness of symbols and meanings in
user interfaces
We need a Semiotic Web
or at least a better understanding of
the semiotics of the web
Thanks
• RC UK, EPSRC, JISC for funding
• Colleagues and Students from the
Schools of Chemistry, Electronics
& Computer Science,
Mathematics
• IBM, Microsoft
• www.combechem.org
• www.ecrystals.soton.ac.uk
• chemtools.chem.soton.ac.uk
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