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Knowledge Graph Construction

Wiki Page: KG-Construction

Purpose

Describe the different parameters and arguments that can be passed when using PheKnowLator to build a knowledge graph. The different options include: build type, construction approach, relation or edge directionality, node metadata use, and decoding of owl semantics. Each of these parameters is explained below.


Build Type

The knowledge graph build algorithm has been designed to run from three different stages of development: full, partial, and post-closure.

Build Type Description Use Cases
full Runs all build steps in the algorithm You want to build a knowledge graph and will not use a reasoner.
partial Runs all of the build steps in the algorithm through adding the edges

Node metadata can always be added to a partial built knowledge graph by running the build as post-closure		 You want to build a knowledge graph and plan to run a reasoner over it.

You want to build a knowledge graph, but do not want to include node metadata, filter OWL semantics, or generate triple lists.
post-closure Assumes that a reasoner was run over a knowledge graph and that the remaining build steps should be applied to a closed knowledge graph. The remaining build steps include determining whether OWL semantics should be filtered and creating and writing triple lists.

If this option is chosen, place the closed knowledge graph .owl file in the resources/knowledge_graphs/relations_only/ or resources/knowledge_graphs/relations_only/ directory (depending on how the graph was built).		 You have run the partial build, ran a reasoner over it, and now want to complete the algorithm.

You want to use the algorithm to process metadata and OWL semantics for an externally built knowledge graph.

Construction Approach

New data can be added to the knowledge graph using 2 different construction approaches: (1) instance-based or (2) subclass-based. Please see this README.md for more information.


Relations/Edge Directionality

PheKnowLator can be built using a single set of provided relations (i.e. the owl:ObjectProperty or edge which is used to connect the nodes in the graph) with or without the inclusion of each relation's inverse. Please see this README.md for additional information.


Node Metadata

The knowledge graph can be built with or without the inclusion of instance node metadata (i.e. labels, descriptions or definitions, and, synonyms). Please see this README.md for additional information.


Decoding OWL Semantics

The knowledge graph can be built with or without the inclusion of edges that contain OWL Semantics. Please see this README.md for additional information.


🛑 ASSUMPTIONS 🛑
The algorithm makes the following assumptions:

  • Edge list data has been created (see here for additional information)
  • Ontologies have been preprocessed (see here for additional information)
  • Decisions made and required input documentation provided for each of the parameters described above.