Building Knowledge Bases
Compositionally
Bruce Porter, Peter Clark
Ken Barker, Art Souther, John Thompson
James Fan, Dan Tecuci, Peter Yeh
Marwan Elrakabawy, Sarah Tierney
Our Approach to RKF
• Our goal: SME’s build knowledge bases by simply
instantiating and assembling pre-built components.
• Our approach: We build a Component Library
containing representations of domain-specific
concepts as well as common:
 actions, such as Get and Enter
 states, such as Be-Attached-To
 entities, such as Barrier and Catalyst
 property values, such as three microns and rapid
And we develop computational methods for:
 combining them and
 using them to answer questions.
Generic Actions
• About 200 actions, in about 20 clusters, based on
linguistic studies and other KB projects
• Are these sufficient?
– Yes, based on an analysis of 6 chapters of the Alberts
text and the encoding of much of chapter 7
– To test their coverage outside microbiology, we’ll be
building dozens of KB’s this semester
– Our Component Evaluation will provide hard data
• Why keep it small?
– So the Library will be easy to learn and use
– So we can provide rich semantics for each action
Generic States
• A state, such as Be-Attached-To, represents
a “temporarily stable” set of properties. It
serves to link:
– An action that creates the state (i.e. Attach)
– An action that ends the state (i.e. Detach)
– Those actions that are affected by the state (e.g.
Move)
Generic Entities
• small number of role concepts, defined by
their participation in actions or states.
Examples: container, sequence, nutrient,
portal, portal covering
Generic Relations
• small number (78) of very general relations
– Roles, such as agent, object, instrument, location
– Properties, such as size, shape, frequency,
direction
• Why keep it small?
– So the Library will be easy to learn and use
– So we can provide rich semantics for each
relation
An Example:
Bacterial RNA Transcription
• main participants
bacterial dna, rna polymerase, rna transcript
• scenario
–
–
–
–
polymerase makes contact with dna
polymerase moves along dna
polymerase recognizes promoter
polymerase transcribes gene, moving along
DNA until it reaches terminator
– transcript detaches from polymerase
– polymerase breaks contact with dna
Participants from Pump Priming
• bacterial dna, rna polymerase, rna transcript
– in the domain-specific hierarchy
• example
– Bacterial-DNA has
location: a Place
regions: a Gene (abuts the Promoter region)
(abuts the Terminator region)
a Promoter
a Terminator
etc.
Events in the Process from the
“Component Library”
• example: Make-Contact
– aka touch, adjoin, meet, contact
Make-Contact
object
destination
location
location
Entity
object
Entity
Move
destination
source
object
Move
object
Be-Touching
source
Place
Place
destination
Place
Bacterial RNA Transcription
Bacterial-RNA-Transcription-Scenario
object
result
causer
Bacterial-DNA
RNA-Polymerase
location
regions
Place
Promoter
Gene
Terminator
RNA-Transcript
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
destination
Bacterial-DNA
RNA-Polymerase
location
object
location
Be-Touching
regions
Place
Promoter
Gene
Terminator
RNA-Transcript
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
source
object
path
destination
Bacterial-DNA
RNA-Polymerase
location
object
location
Be-Touching
regions
Place
Promoter
Gene
Terminator
RNA-Transcript
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
source
object
path
destination
Bacterial-DNA
RNA-Polymerase
location
object
Be-Touching
regions
Place
Promoter
Gene
Terminator
location
RNA-Transcript
Bacterial RNA Transcription
Make-Contact
Move
Recognize
object
Bacterial-DNA
Transcribe
location
object
Be-Touching
Place
Promoter
Gene
Break-Contact
causer
RNA-Polymerase
regions
Detach
Terminator
location
RNA-Transcript
Bacterial RNA Transcription
Make-Contact
Move
Recognize
object
Transcribe
Detach
causer
Break-Contact
result
subevent
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
object
location
Move
object
Be-Touching
regions
location
dest
Place
Promoter
Gene
Terminator
source
Bacterial RNA Transcription
Make-Contact
Move
Recognize
object
Transcribe
Detach
causer
Break-Contact
result
subevent
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
object
location
Move
object
Be-Touching
regions
location
dest
Place
Promoter
Gene
Terminator
source
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
object
Break-Contact
object
location
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
object
Be-Touching
regions
Place
Promoter
Gene
Terminator
object
location
Be-Attached-To
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
object
Break-Contact
object
location
Bacterial-DNA
RNA-Polymerase
location
object
Be-Touching
regions
Place
Promoter
Gene
Terminator
location
RNA-Transcript
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
object
Be-Touching
regions
Place
location
location
Promoter
Gene
Terminator
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
object
Be-Touching
regions
Place
location
location
Promoter
Gene
Terminator
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
regions
location
Place
location
Promoter
Gene
Terminator
Summary
• SME assembles a declarative representation from
both generic and domain-specific components
– SME specifies only the components and the links in the
assembly; most of the complexity within components is
kept “under the hood”
• KANAL can “exercise” the declarative
representation, verifying completeness and
consistency
• KM’s simulator can execute the declarative
representation to answer questions