Download Building a Knowledge Base by Telling a Story: An example

Building a Knowledge Base by
Telling a Story: An example
A virus invades a cell in the following way.
First, the virus attaches 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 cell’s DNA replication
machinery …
Steps in Building a KB
1. Enter the name of the thing you want to describe
 Virus-Invades-Cell
2. Select the general type of thing it is.
 Invade
3. Identify the major participants in the process.
 a cell, a virus
4. List the major steps in the story.
Attach, Penetrate, Uncoat, Move, …
5. Identify the major participants in each step.
Attach and Penetrate: the cell, the virus
Uncoat: enzymes, the virus
SHAKEN will help you with these steps, but
and so on.
let’s look at what’s basically happening…
1. Enter the name of the thing
you want to describe
• Any name is fine – you choose.
• But remember that other people will be
building on your work – for example, to
describe a story in which yours is a
component – so make the name meaningful.
• Use hyphens in place of spaces in the name.
2. Select the general type of thing it is
• You can browse a taxonomy of objects and actions
to choose from.
• For each entry in the taxonomy, you can see a
description of it. For example, here’s the
description for Penetrate.
• Choose the most specific entry in the taxonomy
that fits your needs. For example, Invade is better
than the more general term Enter.
3. Identify the major participants
in the process
• SHAKEN will ask you for the invader and
the thing being invaded. You browse the
taxonomy to select virus and cell.
• If the concept you want is not in the
taxonomy, select a more general concept
and you’ll have a chance to refine it later.
4. List the major steps in the process
• Again, browse the taxonomy to select
actions that describe steps in the process.
Don’t worry if the taxonomy omits some
specific process. Just select a more general
process from the taxonomy, and you can
refine its description later.
 select Attach, Penetrate, Release, Move
Note: we wanted “uncoat”,
but it’s not in the taxonomy
Describing each step of Virus-Invades-Cell
When you say that Penetrate, for example, is a step of the
process, SHAKEN will ask you to describe that step, as
illustrated with this dialogue:
Shaken: What is the barrier that is penetrated?
User: The cell membrane of the cell.
Shaken: What is the penetrator?
User: The virus.
Shaken: To more fully describe the Penetrate, you might want
to specify the following information, too:
– the portal through the cell membrane created by the Penetrate
– the steps that comprise the Penetrate
and so on…
How will this look in SHAKEN?
Actually, when you tell a story to SHAKEN, you use graphs not
sentences. Your information might look like this:
Invade
invader
Virus
Virus-Invades-Cell
thing invaded
Cell
subevent
has-part
Attach
penetrator
Penetrate
Release
barrier
Cell-membrane
Move
Specifying relations between
nodes of the graph
• A graph has two types of information:
– nodes, such as penetrate, cell-membrane, and
virus
– Relations, such as subevent, invader, and
barrier, which connect pairs of nodes
• SHAKEN’s dictionary describes the
relations you can use in describing an entity
or a process.