Building a Knowledge Base by Telling a Story: An example

1. 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 …

2. Steps in Building a KB • Enter the name of the thing you want to describe  Virus-Invades-Cell • Select the general type of thing it is.  Invade • Identify the major participants in the process.  a cell, a virus • List the major steps in the story. Attach, Penetrate, Uncoat, Move, … • Identify the major participants in each step. Attach and Penetrate: the cell, the virus Uncoat: enzymes, the virus and so on. SHAKEN will help you with these steps, but let’s look at what’s basically happening…

3. 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.

4. 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.

5. 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.

6. 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

7. 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…

8. 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 thing invaded Virus Virus-Invades-Cell Cell subevent has-part Attach Penetrate Release Move penetrator barrier Cell-membrane

9. 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.