ExEmPLAR Annotated
Nyssa Tucker
2023-07-03
The purpose of this document is to annotate ExEmPLAR’s interface and act as a visual user guide.
1 ExEmPLAR Loading Page
ExEmPLAR is developed by Jon-Michael Beasley while researching towards a PhD at UNC Chapel Hill.
Please cite ExEmPLAR as:
2 Get Started
2.1 Choose a Knowledge Graph
Here, ROBOKOP
2.2 Code & Run Locally
If you are inclined to use your own machines processing power, it is possible to run ExEmPLAR as a local instance.
2.2.2 Run Locally
Directions
3 Query Options
3.1 Template
Several built in options for typical questions are included in a drop down menu.
3.1.1 Menu
Drop Down Top Grey Center Box
3.1.2 Options
Drop Down Options
3.1.3 Selection Updates
Updates Query Structure to Answer Example Questions
3.2 Modify Query
3.2.1 Node Types
Change Node Types
3.2.2 Specify Types of Connections (Edges) Between Nodes
3.2.2.1 Toggle
Toggle to Display Edge Type Specifications
3.2.2.2 Drop Down Menu
Specify Edge Type
3.2.2.3 Menu Options
Examples of Edge Types
3.2.3 Adjust Query Length
Change Count of In Between Nodes
3.2.4 Starting Node
Specify Starting Point for Query
3.2.4.1 Edit to Specify Query Starting Point
Include (or not) Specific Starting Points for Query
3.2.5 Ending Node
Specify End of Query
3.2.5.1 Edit to Specify Query Ending Point
Include (or not) Specific Ending Points for Query
3.2.6 In Between Node(s)
3.2.6.1 Can Specify Type
Specify Intermediate Steps in Query
3.2.6.2 Can Specify Elements
Specify Element in Intermediate Query Nodes
3.3 Check For Terms
3.3.1 Do Terms Exist?
Do terms exist in Knowledge Graph?
3.3.2 Box Appears Confirming (or not)
Yes they do!
3.4 Ask Multiple Sub-Questions in Single Query
Adjust How Many Questions You Ask
3.5 Prepare Results
Results Estimate
3.5.1 Metadata
3.5.1.1 Toggle
Toggle for Metadata in Results
3.5.1.2 Output
Metadata Results Example
3.5.2 Name Query
If using multiple queries this feature may be important
4 Get Results
4.1 Submit and Settings Box
The submit and settings box enables users to save and load query settings files.
Users can also copy the cypher query used to generate these results to save for future use, or to use right away by clicking the neo4j icon which links to the neo4j interface wherein the cypher query can be visualized in the larger network of the knowledge graph.
Grey Submit Box Annotated
4.2 Submit Query
4.3 Results Table & Analytical Features
4.3.1 Protein Names
Example Output
4.3.2 PubMed Abstract CoMentions (select columns)
4.3.2.1 Toggle
Example Output
4.3.2.2 Auto Updates
Example Output
4.3.3 Network Figure (select rows)
Example Output
4.3.4 Degree Weighted Path Count
4.3.4.1 Compute
Example Output
4.3.4.2 Output
Example Output
4.3.5 Maximum edge-specific node degree (ESND)
Example Output