Building Knowledge Bases Compositionally

Bruce Porter, Peter ClarkKen Barker, Art Souther, John

ThompsonJames 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 rapidAnd 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 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

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-Contactdestination

EntityEntity

Place

object

object

Be-Touching

Move

Move

objectPlace

Place

source

source

destination

destination

object

locationlocation

Bacterial RNA Transcription

Bacterial-DNA RNA-Polymerase

Place

location

Bacterial-RNA-Transcription-Scenario

RNA-Transcript

GenePromoter Terminator

regions

causerobject result

Bacterial RNA TranscriptionMake-Contact

Bacterial-DNA RNA-Polymerase

Place

location

object

Be-Touching

location

Move Recognize Transcribe Detach Break-Contact

RNA-Transcript

GenePromoter Terminator

object

destination

regions

Bacterial RNA TranscriptionMake-Contact

Bacterial-DNA RNA-Polymerase

Place

location

object

Be-Touching

location

Move Recognize Transcribe Detach Break-Contact

RNA-Transcript

GenePromoter Terminator

regions

object

source

destination

path

Bacterial RNA TranscriptionMake-Contact

Bacterial-DNA RNA-Polymerase

Place

location

object

Be-Touching location

Move Recognize Transcribe Detach Break-Contact

RNA-Transcript

GenePromoter Terminator

regions

object

source

destination

path

Bacterial RNA TranscriptionMake-Contact

Bacterial-DNA RNA-Polymerase

Place

location

object

Be-Touching location

Move Recognize Transcribe Detach Break-Contact

RNA-Transcript

GenePromoter Terminator

regions

object causer

Bacterial RNA TranscriptionMake-Contact

Bacterial-DNA RNA-Polymerase

Place

location

object

Be-Touching location

Move Recognize Transcribe Detach Break-Contact

RNA-Transcript

GenePromoter Terminator

regions

object causer result

subevent

Move

object

dest

source

Bacterial RNA TranscriptionMake-Contact

Bacterial-DNA RNA-Polymerase

Place

location

object

Be-Touching location

Move Recognize Transcribe Detach Break-Contact

RNA-Transcript

GenePromoter Terminator

regions

object causer result

subevent

Move

object

dest

source

Bacterial RNA TranscriptionMake-Contact

Bacterial-DNA RNA-Polymerase

Place

location

object

Be-Touching location

Move Recognize Transcribe Detach Break-Contact

RNA-Transcript

GenePromoter Terminator

regions

object

location

object

object

Be-Attached-To

Bacterial RNA TranscriptionMake-Contact

Bacterial-DNA RNA-Polymerase

Place

location

object

Be-Touching location

Move Recognize Transcribe Detach Break-Contact

RNA-Transcript

GenePromoter Terminator

regions

object

location

object

Bacterial RNA TranscriptionMake-Contact

Bacterial-DNA RNA-Polymerase

Place

location

object

Be-Touching location

Move Recognize Transcribe Detach Break-Contact

RNA-Transcript

GenePromoter Terminator

regions

location

object

Bacterial RNA TranscriptionMake-Contact

Bacterial-DNA RNA-Polymerase

Place

location

object

Be-Touching location

Move Recognize Transcribe Detach Break-Contact

RNA-Transcript

GenePromoter Terminator

regions

location

object

Bacterial RNA TranscriptionMake-Contact

Bacterial-DNA RNA-Polymerase

Place

location

location

Move Recognize Transcribe Detach Break-Contact

RNA-Transcript

GenePromoter Terminator

regions

location

object

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