Building Knowledge Bases Compositionally

1
Building Knowledge Bases Compositionally

• Bruce Porter, Peter Clark
• Ken Barker, Art Souther, John Thompson
• James Fan, Dan Tecuci, Peter Yeh
• Marwan Elrakabawy, Sarah Tierney

2
Our Approach to RKF

• Our goal SMEs 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.

3
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,
  well be building dozens of KBs 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

4
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)

5
Generic Entities

• small number of role concepts, defined by their
  participation in actions or states. Examples
  container, sequence, nutrient, portal, portal
  covering

6
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

7
An ExampleBacterial RNA Transcription

• main participantsbacterial 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

8
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.

9
Events in the Process from the Component Library

• example Make-Contact
• aka touch, adjoin, meet, contact

Make-Contact
destination
object
Entity
Place
Entity
10
Bacterial RNA Transcription
Bacterial-RNA-Transcription-Scenario
object
result
causer
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
regions
Place
Gene
Promoter
Terminator
11
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
regions
Place
Gene
Promoter
Terminator
12
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
regions
Place
Gene
Promoter
Terminator
13
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
object
Be-Touching
location
regions
Place
Gene
Promoter
Terminator
14
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
causer
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
object
Be-Touching
location
regions
Place
Gene
Promoter
Terminator
15
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
causer
result
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
object
Be-Touching
location
regions
Place
Gene
Promoter
Terminator
16
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
causer
result
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
object
Be-Touching
location
regions
Place
Gene
Promoter
Terminator
17
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
object
location
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
object
Be-Touching
location
regions
Place
Gene
Promoter
Terminator
18
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
object
location
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
object
Be-Touching
location
regions
Place
Gene
Promoter
Terminator
19
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
object
Be-Touching
location
regions
Place
location
Gene
Promoter
Terminator
20
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
object
Be-Touching
location
regions
Place
location
Gene
Promoter
Terminator
21
Bacterial RNA Transcription
Make-Contact
Move
Recognize
Transcribe
Detach
Break-Contact
object
Bacterial-DNA
RNA-Polymerase
RNA-Transcript
location
location
regions
Place
location
Gene
Promoter
Terminator
22
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
• KMs simulator can execute the declarative
  representation to answer questions