WikiDataScape

WikiDataScape is a Cytoscape app for interactive browsing of WikiData. Wikidata is a free and open knowledge base that can be read and edited by both humans and machines, and acts as central storage for structured data. There are several active WikiProjects that are dedicated to annotating biological entities. See: Gene Wiki or ProteinBoxBot.

The purpose of this app is for the query, navigation, and data discovery of linked data, with WikiData as the data source.

Usage

Creating Nodes

There are several ways new nodes can be added.

WikiData Item Search

Click WikiData Item Search in the Apps title menu. Type in an item to search for and hit enter (on your keyboard). Select a result and click Use this item.

WikiData Multi-Item Lookup

This is useful if you have a list of of identifiers and want to add all them at once. For example, you may have a list of Entrez Gene IDs. To add a list of IDs, click WikiData Multi-Item Lookup in the Apps title menu. The text box under Search for External ID Property, can be used to search for the WikiData property defining the identifier used. For example, see the WikiData page for the Entrez Gene ID Property. To search for properties, press enter. Fill in your list of IDs, and click Go!.

Manual Creation

You can also make a node query-able using WikiDataScape by simply

• add a new single string column to your node table called wdid
• create a new node, or click on an existing node and fill in the wdid field in the node table with a valid WikiData entity ID
• right click on the node, and click Lookup under the WikiData submenu

Property Queries

Insert nice example

What Links Here?

WikiData properties are directional. For example a statement about the item for Mount Everest (indicating it is a mountain):

Mount Everest (item) → instance of (property) → mountain (value)

indicates that Mount Everest is an instance of a mountain, and not the other way around. If we wanted to find all entities that are instance of a mountain, we would need to do a "Backlinks" query, AKA What links here?

As an example:

diabetes mellitus (item) → subclass of (property) → glucose metabolism disease (value)

To find all items that are subclass of glucose metabolism disease, first we would create the glucose metabolism disease node (see the Creating Nodes section). Then, highlight the node, right-click, and select Perform "What links here?" query. Then right-click on the node again, and sub-menu called What links here? will be present under the WikiData menu. Click subclass of. All diseases that are subclass of glucose metabolism disease will be drawn into the network.