V2.0

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Release: v2.0 (first official release)

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TODO: ADD WORKFLOW IMAGE HERE

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Release Updates

New Data Sources:

• The Protein Ontology (created a new human version of the Protein Ontology)
• The Uber-Anatomy Ontology
• The Sequence Ontology
• Human Protein Atlas data including transcript expression in cell and tissue types
• Variant data from ClinVar
• Gene-gene interactions from GeneMania
• Included additional data from Reactome and UniProt

New Functionality:

• Added build options (see here for more details): full, partial, and post-closure
• Added options to construct the knowledge graph using a subclass-based or instance-based approach (see here for more information)
• Added Data_Preparation.ipynb Jupyter Notebook to aid in creation of mapping, filtering, and labeling datasets
• Added Ontology_Cleaning.ipynb Jupyter Notebook to aid in cleaning and preprocessing ontology data
• Added generates_dependency_documents.py to assist users with the creation of required input documents
• Knowledge graph can be constructed using primary edges or primary and inverse edges
• Added metadata for instance data nodes to knowledge graph (see here for details)
• Improved reproducibility by providing detailed metadata on all downloaded data sources
• Removed redundant resource download
• Added explicit typing to all functions and class attributes
• Modified OWL-NETS to decode OWL-encoded classes and triples (see here for more information)
• Provide a Networkx MultiDiGraph graph for each full build (.gpickle)
• Added Docker containers to build pkt_kg and to host Neo4J instances for easy querying of pkt_kg knowledge graphs

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Jupyter Notebooks

• Main.ipynb
• Data_Preparation.ipynb
• Ontology_Cleaning.ipynb

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