October 18, 2021

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PKT Human Disease Knowledge Graph Benchmark Builds (v3.0.2)

Build Date: October 18, 2021

The Human Disease Mechanism KG benchmarks were originally built and stored using Google Cloud Platform (GCP) resources (for details and a complete description of this process, see here). As of late 2023, we have moved the KG builds to Zenodo. While the original GCP resources contained all associated files (i.e., all data used and processed to create the KGs), due to the file size upload limits associated with each archive, we have limited the archived data to KGs output, associated metadata, and log files. The list of resources used to build each KG, including their URLs, and date of download, can all be found in the associated logs. Details on how to access these files are provided below.

Resources

• Software Release: GitHub, PyPI, Zenodo
• DockerHub Build: https://hub.docker.com/repository/docker/callahantiff/pheknowlator
• Build Data Sources: https://github.com/callahantiff/PheKnowLator/wiki/v3-Data-Sources

KG Benchmark Builds can also be obtained from Zenodo

• Class Builds
  • Standard Relations
    • OWL: https://zenodo.org/doi/10.5281/zenodo.8184131
    • OWLNETS: https://zenodo.org/doi/10.5281/zenodo.8184133
  • Inverse Relations
    • OWL: https://zenodo.org/doi/10.5281/zenodo.8184135
    • OWLNETS: https://zenodo.org/doi/10.5281/zenodo.8184137
• Instance
  • Standard Relations
    • OWL: https://zenodo.org/doi/10.5281/zenodo.8184139
    • OWLNETS: https://zenodo.org/doi/10.5281/zenodo.8184141
  • Inverse Relations
    • OWL: https://zenodo.org/doi/10.5281/zenodo.8184143
    • OWLNETS: https://zenodo.org/doi/10.5281/zenodo.8184145

Build Data

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🗂 For additional information on the KG file types please see the following Wiki page, which is also available as a download (here). See data_to_download.txt for a complete list of all downloaded build data.

Required Input Documents
See here for a detailed descriptions of these resources.

• resource_info.txt
• edge_source_list.txt
• ontology_source_list.txt

Required Curated Data
Curated data sources are manually created and were designed to support the build. See the Data_Preparation.ipynb for a detailed descriptions of these resources.

• genomic_sequence_ontology_mappings.xlsx
• genomic_typing_dict.pkl
• zooma_tissue_cell_mapping_04JAN2020.xlsx

Build Metadata
The metadata documentation provides details on each downloaded resource including the URL, date of download, and file size. The resources listed in these documents should align to the similarly names files listed in the Required Input Documents section.

• downloaded_build_metadata.txt
• edge_source_metadata.txt
• preprocessed_build_metadata.txt
• ontology_source_metadata.txt
• ontology_cleaning_report.txt

Build Logs
The build logs provide detailed information on each step of the build process as well as statistics on the resulting KG builds.

• pkt_builder_phases12_log.log
• pkt_build_log.log

Knowledge Graph Output

🚨 Scroll to the right 👉 to see all of the available data 🚨

Instance-based Build
Standard Relations		Inverse Relations
OWL	OWL-NETS	OWL	OWL-NETS
Master_Edge_List_Dict.json node_metadata_dict.pkl subclass_map_log.json PheKnowLator_v3.0.2_full_instance_relationsOnly_OWL.nt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWL_AnnotationsOnly.nt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWL_LogicOnly.nt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_instance_relationsOnly_OWL_NodeLabels.txt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWL_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_instance_relationsOnly_OWL_Triples_Integers.txt	Master_Edge_List_Dict.json node_metadata_dict.pkl subclass_map_log.json PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS.nt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_NodeLabels.txt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_Triples_Integers.txt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_decoding_dict.pkl PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_INSTANCE_purified.nt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_NodeLabels.txt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_Triples_Integers.txt PheKnowLator_v3.0.2_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_decoding_dict.pkl	Master_Edge_List_Dict.json node_metadata_dict.pkl subclass_map_log.json PheKnowLator_v3.0.2_full_instance_inverseRelations_OWL.nt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWL_AnnotationsOnly.nt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWL_LogicOnly.nt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_instance_inverseRelations_OWL_NodeLabels.txt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWL_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_instance_inverseRelations_OWL_Triples_Integers.txt	Master_Edge_List_Dict.json node_metadata_dict.pkl subclass_map_log.json PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS.nt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_NodeLabels.txt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_Triples_Integers.txt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_decoding_dict.pkl PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_INSTANCE_purified.nt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_NodeLabels.txt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_Triples_Integers.txt PheKnowLator_v3.0.2_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_decoding_dict.pkl
Class-based Build
Standard Relations		Inverse Relations
OWL	OWL-NETS	OWL	OWL-NETS
Master_Edge_List_Dict.json node_metadata_dict.pkl subclass_map_log.json PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWL.nt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWL_AnnotationsOnly.nt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWL_LogicOnly.nt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWL_NodeLabels.txt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWL_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWL_Triples_Integers.txt	Master_Edge_List_Dict.json node_metadata_dict.pkl subclass_map_log.json PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS.nt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_NodeLabels.txt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_Triples_Integers.txt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_decoding_dict.pkl PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified.nt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_NodeLabels.txt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_Triples_Integers.txt PheKnowLator_v3.0.2_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_decoding_dict.pkl	Master_Edge_List_Dict.json node_metadata_dict.pkl subclass_map_log.json PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWL.nt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWL_AnnotationsOnly.nt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWL_LogicOnly.nt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWL_NodeLabels.txt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWL_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWL_Triples_Integers.txt	Master_Edge_List_Dict.json node_metadata_dict.pkl subclass_map_log.json PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS.nt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_NodeLabels.txt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_Triples_Integers.txt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_decoding_dict.pkl PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified.nt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_NetworkxMultiDiGraph.gpickle PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_NodeLabels.txt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_Triples_Identifiers.txt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_Triples_Integer_Identifier_Map.json PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_Triples_Integers.txt PheKnowLator_v3.0.2_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_decoding_dict.pkl

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