June 01, 2021

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PKT Human Disease Knowledge Graph Benchmark Builds (v2.1.0)

Build Date: June 01, 2021

Please note that all resources linked below redirect to a publicly Google Cloud Storage bucket where all data are publicly accessible. Routing users from this wiki page is perfectly safe and allows us to avoid requiring users to have a Google account and login to download data. If you have any questions or concerns, please email the project maintainer at callahantiff@gmail.com.

📚 For additional information on the builds please see the following README
🗂 For additional information on the KG file types please see the following Wiki page

Required Input Documents

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

Data

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Logs: pkt_builder_phases12_log.log

Original Data	Processed Data
Metadata
downloaded_build_metadata.txt	preprocessed_build_metadata.txt ontology_cleaning_report.txt
Files
9606.protein.links.v11.0.txt COMBINED.DEFAULT_NETWORKS.BP_COMBINING.txt CTD_chem_gene_ixns.tsv CTD_chem_go_enriched.tsv CTD_chemicals_diseases.tsv CTD_genes_pathways.tsv ChEBI2Reactome_All_Levels.txt GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct Homo_sapiens.GRCh38.102.entrez.tsv Homo_sapiens.GRCh38.102.gtf Homo_sapiens.GRCh38.102.uniprot.tsv Homo_sapiens.gene_info ReactomePathways.txt UniProt2Reactome_All_Levels.txt chebi_with_imports.owl clo_with_imports.owl compath_canonical_pathway_mappings.txt curated_gene_disease_associations.tsv disease_mappings.tsv ext_with_imports.owl gene_association.reactome genomic_sequence_ontology_mappings.xlsx genomic_typing_dict.pkl go_with_imports.owl goa_human.gaf hgnc_complete_set.txt hp_with_imports.owl human_pro_classes.html kegg_reactome.csv mesh2021.nt mondo_with_imports.owl names.tsv phenotype.hpoa pr_with_imports.owl promapping.txt proteinatlas_search.tsv pw_with_imports.owl ro_with_imports.owl so_with_imports.owl uniprot-cofactor-catalyst.tab uniprot_identifier_mapping.tab variant_summary.txt vo_with_imports.owl zooma_tissue_cell_mapping_04JAN2020.xlsx	CLINVAR_VARIANT_GENE_DISEASE_PHENOTYPE_EDGES.txt DISEASE_MONDO_MAP.txt ENSEMBL_GENE_ENTREZ_GENE_MAP.txt ENSEMBL_TRANSCRIPT_PROTEIN_ONTOLOGY_MAP.txt ENTREZ_GENE_ENSEMBL_TRANSCRIPT_MAP.txt ENTREZ_GENE_PRO_ONTOLOGY_MAP.txt GENE_SYMBOL_ENSEMBL_TRANSCRIPT_MAP.txt HPA_GTEX_RNA_GENE_PROTEIN_EDGES.txt HPA_GTEx_TISSUE_CELL_MAP.txt HPA_tissues.txt INVERSE_RELATIONS.txt MESH_CHEBI_MAP.txt Merged_gene_rna_protein_identifiers.pkl PHENOTYPE_HPO_MAP.txt PheKnowLator_MergedOntologies.owl REACTOME_PW_GO_MAPPINGS.txt RELATIONS_LABELS.txt SO_GENE_TRANSCRIPT_VARIANT_TYPE_MAPPING.txt STRING_PRO_ONTOLOGY_MAP.txt UNIPROT_ACCESSION_PRO_ONTOLOGY_MAP.txt UNIPROT_PROTEIN_CATALYST.txt UNIPROT_PROTEIN_COFACTOR.txt chebi_with_imports.owl clo_with_imports.owl ensembl_identifier_data_cleaned.txt ext_with_imports.owl go_with_imports.owl hp_with_imports.owl human_pro.owl mondo_with_imports.owl node_metadata_dict.pkl pr_with_imports.owl pw_with_imports.owl ro_with_imports.owl so_with_imports.owl subclass_construction_map.pkl vo_with_imports.owl

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Knowledge Graphs

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

Instance-based Build
Standard Relations		Inverse Relations
OWL	OWL-NETS	OWL	OWL-NETS
Logs
pkt_build_log.log subclass_map_log.json	pkt_build_log.log subclass_map_log.json	pkt_build_log.log subclass_map_log.json>	pkt_build_log.log subclass_map_log.json
Metadata
edge_source_metadata.txt ontology_source_metadata.txt	edge_source_metadata.txt ontology_source_metadata.txt	edge_source_metadata.txt ontology_source_metadata.txt	edge_source_metadata.txt ontology_source_metadata.txt
Data Files
Master_Edge_List_Dict.json PheKnowLator_MergedOntologies.owl PheKnowLator_v2.1.0_full_instance_relationsOnly_OWL.nt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWL_AnnotationsOnly.nt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWL_LogicOnly.nt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_instance_relationsOnly_OWL_NodeLabels.txt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWL_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_instance_relationsOnly_OWL_Triples_Integers.txt node_metadata_dict.pkl	Master_Edge_List_Dict.json PheKnowLator_MergedOntologies.owl PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS.nt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_NodeLabels.txt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_Triples_Integers.txt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_decoding_dict.pkl PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_INSTANCE_purified.nt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_NodeLabels.txt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_Triples_Integers.txt PheKnowLator_v2.1.0_full_instance_relationsOnly_OWLNETS_INSTANCE_purified_decoding_dict.pkl node_metadata_dict.pkl	Master_Edge_List_Dict.json PheKnowLator_MergedOntologies.owl PheKnowLator_v2.1.0_full_instance_inverseRelations_OWL.nt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWL_AnnotationsOnly.nt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWL_LogicOnly.nt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_instance_inverseRelations_OWL_NodeLabels.txt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWL_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_instance_inverseRelations_OWL_Triples_Integers.txt node_metadata_dict.pkl	Master_Edge_List_Dict.json PheKnowLator_MergedOntologies.owl PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS.nt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_NodeLabels.txt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_Triples_Integers.txt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_decoding_dict.pkl PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_INSTANCE_purified.nt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_NodeLabels.txt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_Triples_Integers.txt PheKnowLator_v2.1.0_full_instance_inverseRelations_OWLNETS_INSTANCE_purified_decoding_dict.pkl node_metadata_dict.pkl
Class-based Build
Standard Relations		Inverse Relations
OWL	OWL-NETS	OWL	OWL-NETS
Logs
pkt_build_log.log subclass_map_log.json	pkt_build_log.log subclass_map_log.json	pkt_build_log.log subclass_map_log.json>	pkt_build_log.log subclass_map_log.json
Metadata
edge_source_metadata.txt ontology_source_metadata.txt	edge_source_metadata.txt ontology_source_metadata.txt	edge_source_metadata.txt ontology_source_metadata.txt	edge_source_metadata.txt ontology_source_metadata.txt
Data Files
Master_Edge_List_Dict.json PheKnowLator_MergedOntologies.owl PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWL.nt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWL_AnnotationsOnly.nt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWL_LogicOnly.nt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWL_NodeLabels.txt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWL_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWL_Triples_Integers.txt node_metadata_dict.pkl	Master_Edge_List_Dict.json PheKnowLator_MergedOntologies.owl PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS.nt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_NodeLabels.txt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_Triples_Integers.txt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_decoding_dict.pkl PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified.nt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_NodeLabels.txt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_Triples_Integers.txt PheKnowLator_v2.1.0_full_subclass_relationsOnly_OWLNETS_SUBCLASS_purified_decoding_dict.pkl node_metadata_dict.pkl	Master_Edge_List_Dict.json PheKnowLator_MergedOntologies.owl PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWL.nt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWL_AnnotationsOnly.nt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWL_LogicOnly.nt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWL_NodeLabels.txt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWL_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWL_Triples_Integers.txt node_metadata_dict.pkl	Master_Edge_List_Dict.json PheKnowLator_MergedOntologies.owl PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS.nt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_NodeLabels.txt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_Triples_Integers.txt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_decoding_dict.pkl PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified.nt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_NodeLabels.txt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_Triples_Identifiers.txt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_Triples_Integer_Identifier_Map.json PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_Triples_Integers.txt PheKnowLator_v2.1.0_full_subclass_inverseRelations_OWLNETS_SUBCLASS_purified_decoding_dict.pkl node_metadata_dict.pkl

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