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 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, 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 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

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 Entity Place object Be-Touching Move object Place source destination object location

10. Bacterial RNA Transcription Bacterial-DNARNA-Polymerase Place location Bacterial-RNA-Transcription-Scenario RNA-Transcript GenePromoterTerminator regions causer objectresult

11. Bacterial RNA Transcription Make-Contact Bacterial-DNARNA-Polymerase Place location object Be-Touching location MoveRecognizeTranscribeDetachBreak-Contact RNA-Transcript GenePromoterTerminator object destination regions

12. Bacterial RNA Transcription Make-Contact Bacterial-DNARNA-Polymerase Place location object Be-Touching location MoveRecognizeTranscribeDetachBreak-Contact RNA-Transcript GenePromoterTerminator regions object source destination path

13. Bacterial RNA Transcription Make-Contact Bacterial-DNARNA-Polymerase Place location object Be-Touching location MoveRecognizeTranscribeDetachBreak-Contact RNA-Transcript GenePromoterTerminator regions object source destination path

14. Bacterial RNA Transcription Make-Contact Bacterial-DNARNA-Polymerase Place location object Be-Touching location MoveRecognizeTranscribeDetachBreak-Contact RNA-Transcript GenePromoterTerminator regions objectcauser

15. Bacterial RNA Transcription Make-Contact Bacterial-DNARNA-Polymerase Place location object Be-Touching location MoveRecognizeTranscribeDetachBreak-Contact RNA-Transcript GenePromoterTerminator regions objectcauserresult subevent Move object dest source

16. Bacterial RNA Transcription Make-Contact Bacterial-DNARNA-Polymerase Place location object Be-Touching location MoveRecognizeTranscribeDetachBreak-Contact RNA-Transcript GenePromoterTerminator regions objectcauserresult subevent Move object dest source

17. Bacterial RNA Transcription Make-Contact Bacterial-DNARNA-Polymerase Place location object Be-Touching location MoveRecognizeTranscribeDetachBreak-Contact RNA-Transcript GenePromoterTerminator regions object location object Be-Attached-To

18. Bacterial RNA Transcription Make-Contact Bacterial-DNARNA-Polymerase Place location object Be-Touching location MoveRecognizeTranscribeDetachBreak-Contact RNA-Transcript GenePromoterTerminator regions object location object

19. Bacterial RNA Transcription Make-Contact Bacterial-DNARNA-Polymerase Place location object Be-Touching location MoveRecognizeTranscribeDetachBreak-Contact RNA-Transcript GenePromoterTerminator regions location object

20. Bacterial RNA Transcription Make-Contact Bacterial-DNARNA-Polymerase Place location object Be-Touching location MoveRecognizeTranscribeDetachBreak-Contact RNA-Transcript GenePromoterTerminator regions location object

21. Bacterial RNA Transcription Make-Contact Bacterial-DNARNA-Polymerase Place location MoveRecognizeTranscribeDetachBreak-Contact RNA-Transcript GenePromoterTerminator regions location object

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