Part I Overview and Introduction to SHAKEN

Simplified Version of how a Virus Invades a Cell “A virus invades a cell in the following way. First, the virus adheres to the cell membrane. It penetrates the membrane and enters the cell cytoplasm. Enzymes in the cytoplasm uncoat the virus, releasing the viral DNA, which then moves into the cell nucleus. Subsequently, the virus takes control of the cell’s DNA replication machinery …”

What is Involved Enter the name of the process you want to describe.  Virus-Invades-Cell Identify major participants in the overall process.  a cell, a virus Identify the major substeps in the process.  adhere, penetrate, enter, uncoat, move, take- control Define each step.  what adhere means: smthg attaches to smthg else Specify the ordering among the substeps Define the role of major participants in each step.  Attach and Penetrate: the cell, the virus  Uncoat: enzymes, the virus

SHAKEN is a good student: it is already quite knowledgeable SHAKEN already knows a few things about biology, for example: –A cell contains cytoplasm. –A virus has a protein coat, contains DNA, etc. SHAKEN also knows a few things about how the world works, for example: –When something moves, it changes location –Entering a container implies moving inside of it NOTE: Today’s SHAKEN is not comprehensive

SHAKEN is a good student: it is proactive SHAKEN will ask you for additional details –Ex: Who is the invader: the cell or the virus? SHAKEN will tell you if something is inconsistent with what it knows –Ex: The virus cannot attach to the cell because it is not located near the cell SHAKEN tries to find solutions to inconsistencies: –Ex: Add a ‘Move’ step before the attach step to change the location of the virus to be near the cell

SHAKEN is a good student: it can be tested for what it knows You can ask questions about what it knows, e.g., –What is/are the agent of a Virus-Invades-Cell ? –During Virus-Invades-Cell, what role does a Cell play? You can ask it to test the process by running a simulation, e.g., –SHAKEN will analyze what happens in each step and tell you about it, e.g., After the virus enters the cell its location is the cytoplasm, The DNA of the virus can be released into the cytoplasm because its container (the Virus) is in the cytoplasm

There is one “minor” problem SHAKEN cannot understand free-flowing English For a computer to understand English is very hard for many reasons: –Understanding: Ambiguity in words, grammar,... –Generating grammatical sentences –Conversational dialogue: anaphora, taking turns,… So instead...

How will this look in SHAKEN? Virus-Invades-Cell Action VirusCell Attach Penetrate Release Move agent object agent Plasma-membrane has-part subevent object participant step role

How to teach this to SHAKEN? 1. Enter the name of the process you want to describe. 2. Define what kind of process it is. 3. Identify major participants in the overall process. 4. Identify the major substeps in the process. 5. Define each step. 6. Specify the ordering among the substeps. 7. Define the role of major participants in each step.

How to teach this to SHAKEN? 1. Enter the name of the process you want to describe. 2. Define what kind of process it is. 3. Identify major participants in the overall process. 4. Identify the major substeps in the process. 5. Define each substep. 6. Specify the ordering among the substeps. 7. Define the role of major participants in each step.

1. Enter the name of the process you want to describe Any name is fine – you choose. But remember that other people may be building on your work – for example, to describe another process where yours will be a component – so make the name meaningful. Use hyphens instead of spaces within the name.

How to teach this to SHAKEN? 1. Enter the name of the process you want to describe. 2. Define what kind of process it is. 3. Identify major participants in the overall process. 4. Identify the major substeps in the process. 5. Define each substep. 6. Specify the ordering among the substeps. 7. Define the role of major participants in each step.

2. Define what kind of process it is Definition is specified in terms of something SHAKEN already knows: –Processes are a kind of action –The agent of an action is the entity that’s responsible for the action, e.g. “the virus invades the cell” –The object of an action is the entity affected by the action, e.g. “the virus invades the cell” –The instrument of an action is the entity used to accomplish the action.

What SHAKEN now knows Virus-Invades-Cell Action agent object

How to teach this to SHAKEN? 1. Enter the name of the process you want to describe. 2. Define what kind of process it is. 3. Identify major participants in the overall process. 4. Identify the major substeps in the process. 5. Define each substep. 6. Specify the ordering among the substeps. 7. Define the role of major participants in each step.

3. Identify the major participants in the process SHAKEN will ask you for the agent and the object. SHAKEN already knows about a few entities that can play a role in a biological process –Virus, cell, DNA, enzyme, etc. –These entities can have parts: e.g. “the cell has-(as)-part a Plasma-Membrane” You can define the role of these entities in the process

What SHAKEN now knows Virus-Invades-Cell Action VirusCell agent object Plasma-membrane has-part

How to teach this to SHAKEN? 1. Enter the name of the process you want to describe. 2. Define what kind of process it is. 3. Identify major participants in the overall process. 4. Identify the major substeps in the process. 5. Define each substep. 6. Specify the ordering among the substeps. 7. Define the role of major participants in each step.

4. Identify the major substeps in the process A virus invades a cell in the following way. First, the virus adheres to the cell membrane. It penetrates the membrane and enters the cell cytoplasm. Enzymes in the cytoplasm uncoat the virus, releasing the viral DNA, which then moves into the cell nucleus.

How to teach this to SHAKEN? 1. Enter the name of the process you want to describe. 2. Define what kind of process it is. 3. Identify major participants in the overall process. 4. Identify the major substeps in the process. 5. Define each substep. 6. Specify the ordering among the substeps. 7. Define the role of major participants in each step.

5. Define each substep Define them in terms of what the system already knows: Move, Enter, Attach, Detach... Each term has a detailed description, such as: Penetrate: The agent creates a portal in the object (a barrier), then passes through the portal, and enters the enclosure. Choose the closest term that can describe the event  Subevents: Attach, Penetrate, Release, Move Note: we wanted “adhere” and “uncoat”, BUT the closest terms available are“attach” and “release”

What SHAKEN now knows Virus-Invades-Cell Action VirusCell Attach Penetrate Release Move agent object subevent

How to teach this to SHAKEN? 1. Enter the name of the process you want to describe. 2. Define what kind of process it is. 3. Identify major participants in the overall process. 4. Identify the major substeps in the process. 5. Define each substep. 6. Specify the ordering among the substeps. 7. Define the role of major participants in each step.

6. Specify the ordering among substeps What steps need to occur before others –Attach before Penetrate –Penetrate before Release –Release before Move

How to teach this to SHAKEN? 1. Enter the name of the process you want to describe. 2. Define what kind of process it is. 3. Identify major participants in the overall process. 4. Identify the major substeps in the process. 5. Define each substep. 6. Specify the ordering among the substeps. 7. Define the role of major participants in each step.

7. Define the role of the major participants at each substep Penetrate has two roles for participants: –agent –object (must be a barrier)

What SHAKEN now knows Virus-Invades-Cell Action VirusCell Attach Penetrate Release Move agent object Plasma-membrane has-part subevent agent

How will you know you taught SHAKEN the right things? You can see things in the screen in front of you, but are they the right things? You can ask SHAKEN to test the process description by running a simulation Ex: During the simulation of a Virus-Invades-Cell, is each step executed properly? You can ask questions Ex: During a Virus-Invades-Cell, what role does a Cell play? –In Virus-Invades-Cell, it is the object –In Move, its nucleus is the destination –In Take-Control, it is the object

Testing with Simulation Summary of the simulation of Virus-Invades-Cell Attach  Penetrate  Release  Move  Take-Control –Attach Checking preconditions : the virus is located near the cell Checking effects: the virus is attached to the cell –Penetrate Checking preconditions :... Checking effects: … –Release... –Move... –Take-Control...

Testing with Questions Choose your question type from a menu, then make it more specific: –What is a Virus-Invades-Cell ? –What is/are the agent of a Virus-Invades-Cell ? –During a Virus-Invades-Cell, what role does a Cell play? –During a Virus-Invades-Cell, what happens to the Thing of a Cell? –Questions about objects participating in a Virus- Invades-Cell

How Do You Know You Are Done Teaching SHAKEN? No errors are reported when you run the simulation You ask a few key questions and the answers are as you expected

Summary SHAKEN’s knowledge is organized in actions and objects Each term that SHAKEN knows about is called a component (Move, Attach, Cell, etc.) Teaching SHAKEN amounts to integrating together existing components that the system knows about –Knowledge entry by composition