DAY 2 Part I: Review Part II: Task Part III: Feedback and Suggestions

DAY 2

Part I: Review

Part II: Task

Part III: Feedback and Suggestions

Before We Start:

Quick Review1. 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.

Component: Penetrate

Virus-Invades-Cell

Action

Virus Cell

Attach Penetrate Release Move

agent object

object

Plasma-membrane

has-partsubevent

agent

“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.”

A Few Comments

• Draw (and read) arrows begin to end

• Hidden does not mean deleted

• Do not drop events into entities and viceversa

• Be cautious before you click: no deletions!

Reading the Graph

Virus-Invades-Cell

Action

Virus Cell

Attach Penetrate Release Move

agent object

object

Plasma-membrane

has-partsubevent

agent

Before We Start:

A Few More Things that SHAKEN Knows About

– Penetrate– Move– Attach– Release– Detach– Transcribe– Make-Contact– Break-Contact– Move (also used above)

– (and many more)

– Virus

– Cell, membrane, cytoplasm, nucleus

– DNA, RNA

– Enzyme

– RNA-Polymerase

– Promoter

– Terminator

– (and many more)

Transcribe (English)

• Move along an information-bearing object making a copy of its information.

Transcribe (definition, contd.)

• Required slot: object • Restriction: an information-bearing object

• Required slot: result• Restriction: a Tangible-Entity that expresses the same information

as the object

• Primary slot: agent • Restriction: causes object to be transcribed

• Primary slot: source• Restriction: a Place

• Primary slot: destination• Restriction: a Place

• Example: “chapters 2 through 6 of the book were transcribed”

object = “the book”

source = “chapter 2” ; destination = “chapter 6”

Transcribe (graph)

Yolanda: This graph will be confusing. The “direct object of the change” should be“object” or “the entity that’s transcribed”.

Make-Contact (English)

• Definition: Two objects come into contact resulting in the objects touching.

• Two cases: – symmetric objects, such as billiard balls– asymmetric objects, such as a fist and a wall SHAKEN uses Make-Contact for both senses of

the term

Make-Contact (definition)

• Required slot: object • Restriction: a Tangible-Entity

• Primary slot: destination• Restriction: a Tangible-Entity

– Examples:• “two cars collided in the parking lot” (symmetric case) a Make-Contact with object = “the two cars”• “the ball hit the windshield” (asymmetric case) a Make-Contact with object = the ball and destination = the windshield

Make-Contact (graph)

Yolanda: again, I’m having trouble with The cmap versions of the components. ThisOne should have the relation object (becauseIt’s a required slot) and offer the SME accessTo destination and the other primary slots. What to do for now? I suggest using the Graph on the next slide.

Make-Contact (graph)

Make-Contact

Tangible-entity Tangible-Entity

object

Make-Contact

Tangible-entity Tangible-Entity

object destination

Symmetric case Asymmetric case

Yolanda: these 2 cmaps could be combined, if you’d like. The combinedVersion would have 3 arcs from Make-Contact, labeled object, object, anddestination. The filler for each relation would be a Tangible-Entity.

Break-Contact (English)

Two objects that are touching at a location cease to be in contact.

Break-Contact (definition)

• Definition: two objects cease contact resulting in the objects no longer touching

• Required slot: object • Restriction: exactly 2 Tangible-Entities

• Primary slot: location • Restriction: Place

• Primary slot: agent • Restriction: causes object’s to Break-Contact

Break-Contact (graph)

Yolanda: Oops, I think this Cmap is wrong. Break-Contact terminates the Be-TouchingState; it doesn’t create it. I’ll draw a new graphOn the next slide

Break-Contact

Break-Contact

Tangible-Entity Tangible-Entity

object

Move (English)

• Change an object’s location

Yolanda: we changed (simplified) the scenario to use Move, not Move-Through. So, you can (re-)use the Definition and cmap for Move that you used for the Virus-Invades-Cell scenario. Note that Move-Through Is a Move with a path specified. So, when you re-show The Move spec, point out the path slot.

Yolanda: Art and I suggest that you omit the next set of slides, I.e. the ones that show: RNA, RNA-Polymerase, Promoter, Terminator, DNA, and Enzyme.

The content of these components, as shown in the graphs, is vacuous. (Art is workingOn “real” versions.) Furthermore, the scenario does not need any of the details shown In the graphs. However, the scenario does need one detail that’s NOT in the graphs, namely: (every DNA has (region ((a Promoter) (a Gene) (a Terminator))))Graphically, you might show this for DNA:

DNA

Promoter Gene Terminator

region

RNA (graph)

RNA-Polymerase (graph)

Promoter (graph)

Terminator (graph)

DNA (definition)

A very, very, very simple one:

• location: a place

DNA (graph)

Enzyme (definition)

A very, very, very simple one:

• has-part: amino-acid

• has-part: carboxy-terminal-end

• has-part: amino-terminal-end

• location: a place

Enzyme (graph)

Your Task Today: Teach SHAKEN about RNA Transcription

RNA polymerase collides with the DNA at some random site. It slides rapidly along the DNA until it encounters a promoter. At that point, it transcribes the DNA until reaching the terminator. Then, the polymerase releases the newly transcribed mRNA and detaches from the DNA.

Your Task Today• This task should take a few hours (1 or 2?)

– You don’t have to hurry, speed is not important

• When is it done:– When you are satisfied with SHAKEN’s answers– When SHAKEN reports no errors

• Try to figure out how to do things instead of asking us a question

• If you really do not know how to proceed, please ask us– Forgive us if we give you just a hint. – Using that hint, try to figure out how to proceed. – Ask for more help if you still cannot figure it out.

Questionnaire and Feedback