Overview of the PheKnowLator Ecosystem

This figure provides an overview of the (Phenotype Knowledge TransLator) Ecosystem. The Ecosystem consists of three components as indicated by the three gray boxes: (1) Knowledge Graph Construction Resources. This component consists of tools to download and process a wide variety of heterogeneous data sources and an algorithm to customize the construction of large-scale biomedical knowledge graphs; (2) Knowledge Graph Tools. This component consists of tools to use knowledge graphs, which include Jupyter Notebook-based use cases and tutorials, Cloud-based storage and APIs, and triplestores; and (3) Knowledge Graph Benchmarks. This component consists of benchmarks that can be used to assess knowledge graph construction and data source decisions, compare against existing knowledge graphs, and evaluate downstream analyses, workflows, and learning algorithms designed for knowledge graphs. Acronyms: NT (N-Triples file format); OWL (Web Ontology Language); PKL (Python pickle file format); SPARQL (SPARQL Protocol and RDF Query Language).