Knowledge Base Content
Bruce Porter, Peter Clark
Ken Barker, Art Souther, John Thompson
James Fan, Dan Tecuci, Peter Yeh
Marwan Elrakabawy, Sarah Tierney
Knowledge Base Content
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Generic components
Composition methods
Simulation methods
Domain-specific components
Extended scenarios
http://www.cs.utexas.edu/users/mfkb/RKF
What’s in a Component?
• The specification gives the definition, slot
constraints, and links to standard linguistic
sources. Here’s an example.
• The KM code gives the axioms and an
explicit interface to the user. Here’s an
example. Note that the code includes only
local axioms; KM infers the rest.
http://www.cs.utexas.edu/users/mfkb/RKF
Our Process for Building a Component
• form initial clusters of actions (e.g. transfer) based on an analysis
of Alberts, Roget’s clusters, Cyc, and other linguistic sources.
• write a specification for each action.
• search Alberts for all occurrences (including all morphological
variants) of each action, and make sure that the representation
will accommodate them. Here’s the result of analyzing the
actions in one chapter. These “coded examples”will be useful for
training SME’s.
• organize the actions taxonomically and pull out commonalities
that can be handled with various types of composition.*
• code the actions in KM along with simple test cases, commit
them to the CVS-managed library, and run all test cases daily.
Larger scenarios provide the next level: integration testing.*
* These points will be elaborated below.
How do Components Compose?
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inheritance
clichés
utility concepts
modeling
Non-taxonomic composition:
Clichés
• a cliché is a small pattern of axioms that recurs throughout the
hierarchy. For example:
• Reflexive:
requiredslot: agent, object
agent=object
• Reciprocal:
requiredslot: agent, object
agent is object of an instance of this action
having this object as agent
• Undo(A):
precondition: object is the object of the
resulting-state of action A
postcondition: object is no longer the object of the
resulting-state of action A
Non-taxonomic composition:
Utility Concepts
• concepts that have natural homes within the
hierarchy, but also form a part of the
semantics of concepts across the hierarchy
• Copy:
– reasonable as a standalone concept
– also part of Transcribe, Forge, Encode,
Reproduce, etc.
Non-taxonomic composition:
model-as
• Many concepts in the KB are “role concepts”
– e.g., container, nutrient
– are generic
– are highly reusable (can be applied in many concepts)
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“If the DNA containing the 5S rRNA genes is …”
“many DNA sequences produce two or more distinct proteins”
“The DNA guides the synthesis of specific RNA molecules…”
“The DNA is enclosed in …”
“The idea that DNA transfers information…”
• By separating the “model” (e.g. container) and its
application (e.g. to DNA), we can apply & reuse the
same model in many ways.
Applying models
• Traditional: “Hard-wire” models to the modeled things
Cell
generalizations: Container Consumer …?
• Better: Define machine-selectable “views”
Cell
model-as: Container (wall = membrane, ..)
Consumer (consumes = organic molecules, ..)
Vehicle (transported = DNA, …)
….
• Control when and how components apply
• Allows generic components to be used multiple ways
(more reuse) - difficult in the traditional approach!
A Role Concept: Container
Entity
object
the-container
Move-Out-Of
source
path
Portal
Container
location
Place
has-part
is-inside
is-between
Place
Place
is-outside
destination
Wall
has-part
object
Be-Blocked
instrument
implies
Portal-Covering
object
Be-Closed
Example of Composition
“eucaryotic mRNA exits the cell nucleus”
• composition triggered automatically through Exit
– inheritance
• location of mRNA changes from inside nucleus to outside
– cliché
• mRNA is the mover and the moved (Exit is reflexive)
– modeling
• cell nucleus as a container
– has an inside, an outside, a wall, portals, etc.
Example
Exit
Entity
object
the-container
Move-Out-Of
Container
source
path
Portal
Place
location
is-inside
is-between
Place
Place
is-outside
destination
has-part
Wall
has-part
Portal-Covering
Example
Eucaryotic-MRNA
Exit
object
path
source
the-container
Entity
Container
Place
destination
Portal
location
is-inside
is-between
Place
Place
is-outside
has-part
Wall
has-part
Portal-Covering
Example
Nuclear-Envelope
agent
Eucaryotic-MRNA
has-part
object
path
Exit
source
Cell-Nucleus
the-container
Container
Place
destination
Portal
location
is-inside
is-between
Place
Place
is-outside
has-part
Wall
has-part
Portal-Covering
Example
Nuclear-Envelope
agent
Eucaryotic-MRNA
has-part
object
path
Exit
the-container
Cell-Nucleus
source
has-part
location
Place
destination
Portal
is-inside
is-between
Place
Place
is-outside
Wall
has-part
Portal-Covering
Example
Nuclear-Envelope
agent
Eucaryotic-MRNA
has-part
object
path
Exit
the-container
Cell-Nucleus
source
location
destination
Portal
Place
is-inside
is-between
Place
Place
is-outside
has-part
Portal-Covering
Answering Questions via
Simulation
• To reason about change over time, KM builds a
graph of actions and states
Global contains timeinvariant descriptions
G
S1
A
S3
S1.1
S1.2
S2
Action A transforms
State1 into State2
S3 describes ‘the world’ during A
These states show S1 ‘under a microscope’
• KM’s simulation is discrete, and we’re using KM
just for normative models. We’re integrating KM with
Cohen’s continuous simulators to handle other models.
Pump-Priming Knowledge
• Our goals for pump priming:
– Define the terms used in chapter 7, but
introduced earlier
– Provide the ‘common sense’ knowledge that
motivates the process of protein synthesis
• Our approach is to develop:
– Partonomies and taxonomies for entities and
processes
– Numerous scenarios related to protein synthesis
Example Scenarios
• The role of proteins in cell metabolism
• The overall function of cells and how the
functions are affected by protein synthesis
• The role of protein synthesis in cell adaptation
• The role of primary and secondary structure
• Enzyme kinetics, diffusion, bonding, and
energy coupling