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: 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 Andwe 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, 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

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 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

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 Terminatoretc.

9. location location object destination Move source object Place Move object source destination Be-Touching Place Events in the Process from the “Component Library” • example:Make-Contact • akatouch, 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 Promoter Gene Terminator

11. object destination object location Be-Touching Bacterial RNA Transcription Make-Contact Move Recognize Transcribe Detach Break-Contact Bacterial-DNA RNA-Polymerase RNA-Transcript location regions Place Promoter Gene Terminator

12. source object path destination object location Be-Touching Bacterial RNA Transcription Make-Contact Move Recognize Transcribe Detach Break-Contact Bacterial-DNA RNA-Polymerase RNA-Transcript location regions Place Promoter Gene Terminator

13. source object path destination Bacterial RNA Transcription Make-Contact Move Recognize Transcribe Detach Break-Contact Bacterial-DNA RNA-Polymerase RNA-Transcript location object Be-Touching regions location Place Promoter Gene 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 regions location Place Promoter Gene Terminator

15. subevent object Move dest source Bacterial RNA Transcription Make-Contact Move Recognize Transcribe Detach Break-Contact object causer result Bacterial-DNA RNA-Polymerase RNA-Transcript location object Be-Touching regions location Place Promoter Gene Terminator

16. subevent object Move dest source Bacterial RNA Transcription Make-Contact Move Recognize Transcribe Detach Break-Contact object causer result Bacterial-DNA RNA-Polymerase RNA-Transcript location object Be-Touching regions location Place Promoter Gene Terminator

17. object Be-Attached-To Bacterial RNA Transcription Make-Contact Move Recognize Transcribe Detach Break-Contact object object location Bacterial-DNA RNA-Polymerase RNA-Transcript location object Be-Touching regions location Place Promoter Gene 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 regions location Place Promoter Gene Terminator

19. Bacterial RNA Transcription Make-Contact Move Recognize Transcribe Detach Break-Contact object Bacterial-DNA RNA-Polymerase RNA-Transcript location object Be-Touching regions location Place location Promoter Gene Terminator

20. Bacterial RNA Transcription Make-Contact Move Recognize Transcribe Detach Break-Contact object Bacterial-DNA RNA-Polymerase RNA-Transcript location object Be-Touching regions location Place location Promoter Gene Terminator

21. 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

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 • KM’s simulator can execute the declarative representation to answer questions