1. Knowledge Engineering from
Experimental Design
‘KEfED’
Gully APC Burns
Information Sciences Institute
University of Southern California
2. The Cycle of Scientific
Investigation (‘CoSI’)
Knowledge Engineering from
Experimental Design
3. What is an elemental piece
of biomedical scientific knowledge?
A typical seminar slide
4. What is an elemental piece
of biomedical scientific knowledge?
For example...
5. The challenge of defining the
biomedical semantic web
• Currently consists of a very large number of statements like ‘mice
like cheese’
– semantics at this level are complicated!
• For example:
– “Novel neurotrophic factor CDNF protects midbrain dopamine neurons
in vivo” [Lindholm et al 2007]
– “Hippocampo-hypothalamic connections: origin in subicular cortex,
not ammon's horn.” [Swanson & Cowan 1975]
– “Intravenous 2-deoxy-D-glucose injection rapidly elevates levels of the
phosphorylated forms of p44/42 mitogen-activated protein kinases
(extracellularly regulated kinases 1/2) in rat hypothalamic
parvicellular paraventricular neurons.” [Khan & Watts 2004]
• Statements vary in their levels of reliability, specificity.
• Existing semantic web approaches involve representations of
argumentation / claim networks
• Can we invent a new way to introduce formalism?
6. Knowledge Engineering from
Experimental Design (‘KEfED’)
• There is an implicit reasoning model employed
by scientists to represent their observations
based on the way they design experiments
– Standardized experimental templates
– Parameters [‘Independent Variables’]
– Measurements [‘Dependent Variables’]
– Calculations [‘Derived Variables’]
7. Basic KEfED Elements
Logical Element Icon
Activity
Experimental Object
Parameter
Measurement
Branch
Fork
12. Example : Neural Connectivity -
Observations
Tract Tracing Experiments
Neuroanatomical experiments to study neural connectivity.
labeling-density
‘anterograde’
tracer-chemical
injection-site
labeling-location
‘retrograde’
labeling-type
13. Example : Neural Connectivity -
Interpretations
Tract Tracing Experiments > Neuroanatomical Elements
Interpretative entities that correspond to facts that may be aggregated into a model
connection-
‘Neural Connection’ strength
connection-
connection- termination
origin
terminal-field
Neuronal Population
cell-bodies.location
cell-bodies
terminal-field.location
14. 1st look at ‘BioScholar system’:
Neural Connectivity Reasoning Tool
15. 1st look at ‘BioScholar system’:
Neural Connectivity Reasoning Tool
16. Peeking Under the Hood
‘PHAL Injection into SUBv generates labeling in MM’
=> ‘SUBv contains neurons that project to MM’
(expressed in First-Order-Logic within Powerloom Reasoner)
Computation
based on the
context of each
measurement
based on
parameters
17. Crux
• KEfED as the basis for the design of a
data repository
• Collaboration with MSU + Science
Commons
– Funded by MJFF + Kinetics Foundation to
manage data from grantees
• KEfED-editor can as a component in an
external web-application
[http://yogo.msu.montana.edu/applications/crux.html]
18. Using Semantic Web Standards
[https://wiki.birncommunity.org:8443/display/NEWBIRNCC/KEfED+OWL+Model]
19. OBI
• Use a simplified ‘projection’
with no semantic
entailments.
• Seek a simple model with
semantics embedded
‘within’ variables
… work in progress here …
• Seek semantic-web-based
links to:
– OBI
– SWAN / SIOC
– ISA-Tab tools
• Domain-specific Reasoning
Models (from ‘CoSI’)
– Want to generate
hypotheses /
predictions that can be
expressed as KEfED
models?
– $6,000,000 question!
21. Acknowledgements
Funding Computer Scientist Team
– Information Sciences Institute, – Tom Russ (ISI)
seed funding – Cartic Ramakrishnan (ISI)
– NIGMS (R01GM083871) – Marcelo Tallis (ISI)
– NIMH (R01MH079068) – Eduard Hovy (ISI)
– NSF (#0849977)
– Michael J Fox + Kinetics Other Team members
Foundations
– Alan Ruttenberg (ScienceCommons)
– BIRN @ ISI
– Michael Rogan (NYU)
– Gwen Jacobs (MSU)
Neuroscience Team Members – Pol Llovet (MSU)
– Rick Thompson (USC)
– Jessica Turner (MRN) Computer Scientist Contributors
– Hans Chalupsky (ISI)
Neuroscience Contributors – Jerry Hobbs (ISI)
– Alan Watts (USC) – Yolanda Gil (ISI)
– Larry Swanson (USC) – Carl Kesselman (ISI)
– Arshad Khan (USC) – Jose Luis Ambite (ISI)
