FAQ

Q: Are there any requirements for user queries?

A: User can draw customized sub-graph queries and add node property constraints. There can only be one connected component in the query. For example, a four-node query [A–>B, C–>D] is not allowed since two components should be submitted separately.

Q: How can I know where to find a node type (e.g., gene) in the “add node” window?

A: The hierarchical node type/relation type is shown in the tables below.

Q: How can I know more information about a node/relation type? E.g., which other nodes does a gene usually connect to.

A: In Example nodes and edges, users can check the example nodes/relations from all node types.

Q: The database I am interested in is not covered by GenomicKB, is it possible to import it?

A: Currently we do not support users importing their data. But since knowledge graphs are flexible to adapt updates of nodes, relations, and entire data sources, we are open to any new data from well-established data sources. You can suggest our team of new data sources by e-mail, and we are happy to include more!

Q: How many nodes/relations are displayed on the result page?

A: It depends on the complexity of the query. The neo4j backend tries to find sub-graphs that match the user query. At most twenty sub-graphs will be visualized for a one-node query, ten for two-node a query, and five for queries with more nodes. However, two identified sub-graphs might have some overlaps, and therefore ten result sub-graphs of a two-node query do not mean twenty nodes.

Q: How to get a complete result?

A: By clicking “export”, users can download the complete result of the user query. “Export summary” returns the count of all node/relation types, and “export all” returns the complete result graph in Microsoft Excel format.

Q: The “export all” takes a long time.

A: Exporting complete results requires searching the entire knowledge graph (with more than 300 million nodes and 1 billion relations), which is normal to take a longer time. If the waiting time is more than 10 minutes, you can try to narrow down the results by adding node constraints (e.g., chromosomes).