Fig. 8

An Example of How Variant-Disease Edges are Created in the PKT Human Disease Mechanism Knowledge Graph. This figure provides an end-to-end example of how variant-disease edges are created in the PKT Human Disease Mechanism knowledge graph. Beginning with the Data Preparation stage, in Step 1, the primary data source (i.e., ClinVar data) is downloaded and cleaned, which includes steps such as replacing “NaN” values with “None”, removing bad or missing identifiers, unnesting the data, and reformatting identifiers. The cleaned data (highlighted in yellow) are output for ingestion into the Knowledge Graph Construction stage. In Step 2, metadata are extracted from the primary data source to create labels, synonyms, and descriptions for each identifier. Step 3 leverages a manually curated resource (highlighted in green) to map variant identifiers to a PKT core ontology. In this case, variant identifiers are aligned to the Sequence Ontology (SO) by their type, and the final mapping is output to subclass_construction_map.pkl which is one of the required inputs for constructing a knowledge graph (highlighted in purple; cited example is from the May 2021 Class-Standard Relation-OWL build). In Step 4, the final step of this stage, the remaining required input documents for constructing a knowledge graph are updated with the resources created in the prior steps. In the Knowledge Graph Construction stage, the cleaned variant data are downloaded and an edge list is built. This edge list can then be used to construct the 12 different knowledge graphs shown in the bottom right gray box. In this example, the class-based semantically abstracted knowledge graphs are the same whether harmonization is applied or not, which is often the case for class-based builds that leverage Open Biological and Biomedical Ontology Foundry ontologies. See the Data_Preparation.ipynb Jupyter Notebook (https://github.com/callahantiff/PheKnowLator/blob/master/notebooks/Data_Preparation.ipynb) for code to process all resources used in the PKT Human Disease knowledge graph. Acronyms: PKT (PheKnowLator). Note. A UUID is a blank or anonymous node that is created from an md5 hash of concatenated Universal Resource Identifiers (URIs). The URIs used in the hash string include the subject and object URIs (each appended with “subject” and “object,” respectively) in addition to a relation. All UUIDs created during construction are explicitly defined within the PKT namespace (https://github.com/callahantiff/PheKnowLator/pkt/).