1. Knowledge Base Content Bruce Porter, Peter Clark Ken Barker, Art Souther, John Thompson James Fan, Dan Tecuci, Peter Yeh Marwan Elrakabawy, Sarah Tierney

2. Knowledge Base Content Generic components Composition methods Simulation methods Domain-specific components Extended scenarios http://www.cs.utexas.edu/users/mfkb/RKF

3. What’s in a Component? The specification gives the definition, slot constraints, and links to standard linguistic sources. Here’s an example.example The KM code gives the axioms and an explicit interface to the user. Here’s an example. Note that the code includes only local axioms; KM infers the rest. example http://www.cs.utexas.edu/users/mfkb/RKF

4. Our Process for Building a Component form initial clusters of actions (e.g. transfer) based on an analysis of Alberts, Roget’s clusters, Cyc, and other linguistic sources.analysis of AlbertsRoget’s clustersCyc write a specification for each action. search Alberts for all occurrences (including all morphological variants) of each action, and make sure that the representation will accommodate them. Here’s the result of analyzing the actions in one chapter. These “coded examples”will be useful for training SME’s.AlbertsHere’s organize the actions taxonomically and pull out commonalities that can be handled with various types of composition.* code the actions in KM along with simple test cases, commit them to the CVS-managed library, and run all test cases daily. Larger scenarios provide the next level: integration testing.* * These points will be elaborated below.

5. How do Components Compose? inheritance clichés utility concepts modeling

6. Non-taxonomic composition: Clichés a cliché is a small pattern of axioms that recurs throughout the hierarchy. For example:recurs throughout the hierarchy Reflexive: requiredslot: agent, object agent=object Reciprocal: requiredslot: agent, object agent is object of an instance of this action having this object as agent Undo(A): precondition: object is the object of the resulting-state of action A postcondition: object is no longer the object of the resulting-state of action A

7. Non-taxonomic composition: Utility Concepts concepts that have natural homes within the hierarchy, but also form a part of the semantics of concepts across the hierarchyacross the hierarchy Copy: –reasonable as a standalone concept –also part of Transcribe, Forge, Encode, Reproduce, etc.

8. Many concepts in the KB are “role concepts” –e.g., container, nutrient –are generic –are highly reusable (can be applied in many concepts) “If the DNA containing the 5S rRNA genes is …” “many DNA sequences produce two or more distinct proteins” “The DNA guides the synthesis of specific RNA molecules…” “The DNA is enclosed in …” “The idea that DNA transfers information…” By separating the “model” (e.g. container) and its application (e.g. to DNA), we can apply & reuse the same model in many ways. Non-taxonomic composition: model-as

9. Traditional: “Hard-wire” models to the modeled things Applying models Better: Define machine-selectable “views” Cell generalizations: Container Consumer …? Cell model-as: Container (wall = membrane,..) Consumer (consumes = organic molecules,..) Vehicle (transported = DNA, …) …. Control when and how components apply Allows generic components to be used multiple ways (more reuse) - difficult in the traditional approach!

10. A Role Concept: Container Container Place Wall Portal-Covering Place is-inside is-outside location has-part Be-Blocked instrument object Portal Move-Out-Of is-between source destination path Entity object Be-Closed implies the-container

11. Example of Composition composition triggered automatically through Exit –inheritance location of mRNA changes from inside nucleus to outside –cliché mRNA is the mover and the moved (Exit is reflexive) –modeling cell nucleus as a container –has an inside, an outside, a wall, portals, etc. “eucaryotic mRNA exits the cell nucleus”

12. Example Move-Out-Of source destination path objectthe-container EntityContainer location has-part Wall Portal-Covering Place is-inside is-outside Portal is-between Exit

13. object EntityContainer location has-part the-container Wall Example Portal-Covering Place is-inside is-outside Portal is-between ExitEucaryotic-MRNA source path destination

14. Container location has-part the-container Wall Example Portal-Covering Place is-inside is-outside Portal is-between Nuclear-Envelope has-part Cell-Nucleus ExitEucaryotic-MRNA object agent source path destination

15. Wall has-part Example Portal-Covering Place is-inside is-outside Portal is-between Cell-Nucleus Nuclear-Envelope has-part ExitEucaryotic-MRNA objectthe-container agent source path destination has-part location

16. Example Portal-Covering Place is-inside is-outside Portal is-between Cell-Nucleus Nuclear-Envelope has-part ExitEucaryotic-MRNA objectthe-container agent source path destination has-part location

17. Answering Questions via Simulation To reason about change over time, KM builds a graph of actions and states A S1S2 S3 S1.1 S1.2 G Global contains time- invariant descriptions Action A transforms State1 into State2 S3 describes ‘the world’ during A These states show S1 ‘under a microscope’ KM’s simulation is discrete, and we’re using KM just for normative models. We’re integrating KM with Cohen’s continuous simulators to handle other models.

18. Pump-Priming Knowledge Our goals for pump priming: –Define the terms used in chapter 7, but introduced earlier –Provide the ‘common sense’ knowledge that motivates the process of protein synthesis Our approach is to develop: –Partonomies and taxonomies for entities and processes –Numerous scenarios related to protein synthesis

19. Example Scenarios The role of proteins in cell metabolism The overall function of cells and how the functions are affected by protein synthesis The role of protein synthesis in cell adaptation The role of primary and secondary structure Enzyme kinetics, diffusion, bonding, and energy coupling