May 10, 2020

---

PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)

Build Date: May 10, 2020

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.

If you have a Google account you can access the data directly via 👉 here

📚 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

---

Original Data	Processed Data
Metadata
OWL_NETS_Property_Types.txt chemical-gene_GENE_METADATA.txt chemical-pathway_PATHWAY_METADATA.txt chemical-rna_RNA_METADATA.txt gene-disease_GENE_METADATA.txt gene-gene_GENE_METADATA.txt gene-pathway_GENE_METADATA.txt gene-phenotype_GENE_METADATA.txt gene-protein_GENE_METADATA.txt gene-rna_GENE_METADATA.txt genomic_sequence_ontology_mappings.xlsx gobp-pathway_PATHWAY_METADATA.txt pathway-gocc_PATHWAY_METADATA.txt pathway-gomf_PATHWAY_METADATA.txt protein-pathway_PATHWAY_METADATA.txt rna-anatomy_RNA_METADATA.txt rna-cell_RNA_METADATA.txt rna-protein_RNA_METADATA.txt subclass_construction_map.pkl variant-disease_VARIANT_METADATA.txt variant-gene_VARIANT_METADATA.txt variant-phenotype_VARIANT_METADATA.txt	edge_source_metadata.txt ontology_source_metadata.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.GRCh38.99.entrez.tsv Homo_sapiens.GRCh38.99.gtf Homo_sapiens.GRCh38.99.uniprot.tsv Homo_sapiens.gene_info ReactomePathways.txt UniProt2Reactome_All_Levels.txt chebi_lite.owl chebi_lite_with_imports.owl clo_with_imports.owl compath_canonical_pathway_mappings.txt disease_mappings.tsv doid_with_imports.owl ext_with_imports.owl gene_association.reactome genomic_sequence_ontology_mappings.xlsx go_with_imports.owl hgnc_complete_set.txt hp_with_imports.owl human_pro_classes.html human_pro_closed_with_imports.owl kegg_reactome.csv 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	INVERSE_RELATIONS.txt PheKnowLator_MergedOntologiesGeneID_Normalized_Cleaned.owl RELATIONS_LABELS.txt chebi_lite_with_imports.owl chebi_lite_with_imports.owl chemical-disease_CTD_chemicals_diseases.tsv chemical-gene_CTD_chem_gene_ixns.tsv chemical-gene_GENE_METADATA.txt chemical-gobp_CTD_chem_go_enriched.tsv chemical-gocc_CTD_chem_go_enriched.tsv chemical-gomf_CTD_chem_go_enriched.tsv chemical-pathway_ChEBI2Reactome_All_Levels.txt chemical-pathway_PATHWAY_METADATA.txt chemical-phenotype_CTD_chemicals_diseases.tsv chemical-protein_CTD_chem_gene_ixns.tsv chemical-rna_CTD_chem_gene_ixns.tsv chemical-rna_RNA_METADATA.txt clo_with_imports.owl clo_with_imports_clean.owl disease-phenotype_phenotype_annotation.tab doid_with_imports.owl doid_with_imports_clean.owl ext_with_imports.owl ext_with_imports_clean.owl gene-disease_GENE_METADATA.txt gene-disease_curated_gene_disease_associations.tsv gene-gene_COMBINED.DEFAULT_NETWORKS.BP_COMBINING.txt gene-gene_GENE_METADATA.txt gene-pathway_CTD_genes_pathways.tsv gene-pathway_GENE_METADATA.txt gene-phenotype_GENE_METADATA.txt gene-phenotype_curated_gene_disease_associations.tsv gene-protein_ENTREZ_GENE_PRO_ONTOLOGY_MAP.txt gene-protein_GENE_METADATA.txt gene-rna_ENTREZ_GENE_ENSEMBL_TRANSCRIPT_MAP.txt gene-rna_GENE_METADATA.txt go_with_imports.owl go_with_imports_clean.owl gobp-pathway_PATHWAY_METADATA.txt gobp-pathway_gene_association.reactome hp_with_imports.owl hp_with_imports_clean.owl human_pro_closed_with_imports.owl human_pro_closed_with_imports_clean.owl pathway-gocc_PATHWAY_METADATA.txt pathway-gocc_gene_association.reactome pathway-gomf_PATHWAY_METADATA.txt pathway-gomf_gene_association.reactome protein-anatomy_HPA_GTEX_RNA_GENE_PROTEIN_EDGES.txt protein-catalyst_UNIPROT_PROTEIN_CATALYST.txt protein-cell_HPA_GTEX_RNA_GENE_PROTEIN_EDGES.txt protein-cofactor_UNIPROT_PROTEIN_COFACTOR.txt protein-gobp_goa_human.gaf protein-gocc_goa_human.gaf protein-gomf_goa_human.gaf protein-pathway_PATHWAY_METADATA.txt protein-pathway_UniProt2Reactome_All_Levels.txt protein-protein_9606.protein.links.v11.0.txt pw_with_imports.owl pw_with_imports_clean.owl rna-anatomy_HPA_GTEX_RNA_GENE_PROTEIN_EDGES.txt rna-anatomy_RNA_METADATA.txt rna-cell_HPA_GTEX_RNA_GENE_PROTEIN_EDGES.txt rna-cell_RNA_METADATA.txt rna-protein_ENSEMBL_TRANSCRIPT_PROTEIN_ONTOLOGY_MAP.txt rna-protein_RNA_METADATA.txt ro_with_imports.owl ro_with_imports_clean.owl so_with_imports.owl so_with_imports_clean.owl subclass_construction_map.pkl variant-disease_CLINVAR_VARIANT_GENE_DISEASE_PHENOTYPE_EDGES.txt variant-disease_VARIANT_METADATA.txt variant-gene_CLINVAR_VARIANT_GENE_DISEASE_PHENOTYPE_EDGES.txt variant-gene_VARIANT_METADATA.txt variant-phenotype_CLINVAR_VARIANT_GENE_DISEASE_PHENOTYPE_EDGES.txt variant-phenotype_VARIANT_METADATA.txt vo_with_imports.owl vo_with_imports_clean.owl

---

---

Knowledge Graphs

---

🚨 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
PheKnowLator_v2.0.0_full_Instance_relationsOnly_OWL_Stats.txt PheKnowLator_v2.0.0_full_Instance_relationsOnly_OWL_Stats_Terminal_Output.txt subclass_map_log.json	PheKnowLator_v2.0.0_full_Instance_relationsOnly_noOWL_Stats.txt PheKnowLator_v2.0.0_full_Instance_relationsOnly_noOWL_Stats_Terminal_Output.txt subclass_map_log.json	PheKnowLator_v2.0.0_full_Instance_inverseRelations_OWL_Stats.txt PheKnowLator_v2.0.0_full_Instance_inverseRelations_OWL_Stats_Terminal_Output.txt subclass_map_log.json>	PheKnowLator_v2.0.0_full_Instance_inverseRelations_noOWL_Stats.txt PheKnowLator_v2.0.0_full_Instance_inverseRelations_noOWL_Stats_Terminal_Output.txt 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_Master_Node_Edge_List_Dict.json PheKnowLator_MergedOntologiesGeneID_Normalized_Cleaned.owl PheKnowLator_v2.0.0_full_relationsOnly_OWL.owl PheKnowLator_v2.0.0_full_Instance_relationsOnly_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.0.0_full_Instance_relationsOnly_OWL_NodeLabels.txt PheKnowLator_v2.0.0_full_Instance_relationsOnly_OWL_Triples_Identifiers.txt PheKnowLator_v2.0.0_full_Instance_relationsOnly_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.0.0_full_Instance_relationsOnly_OWL_Triples_Integers.txt	Master_Edge_List_Dict.json PheKnowLator_Master_Node_Edge_List_Dict.json PheKnowLator_MergedOntologiesGeneID_Normalized_Cleaned.owl PheKnowLator_v2.0.0_full_Instance_relationsOnly_OWL.owl PheKnowLator_v2.0.0_full_Instance_relationsOnly_noOWL_NodeLabels.txt PheKnowLator_v2.0.0_full_Instance_relationsOnly_noOWL_OWLNETS.nt PheKnowLator_v2.0.0_full_Instance_relationsOnly_noOWL_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.0.0_full_Instance_relationsOnly_noOWL_Triples_Identifiers.txt PheKnowLator_v2.0.0_full_Instance_relationsOnly_noOWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.0.0_full_Instance_relationsOnly_noOWL_Triples_Integers.txt	Master_Edge_List_Dict.json PheKnowLator_Master_Node_Edge_List_Dict.json PheKnowLator_MergedOntologiesGeneID_Normalized_Cleaned.owl PheKnowLator_v2.0.0_full_inverseRelations_OWL.owl PheKnowLator_v2.0.0_full_Instance_inverseRelations_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.0.0_full_Instance_inverseRelations_OWL_NodeLabels.txt PheKnowLator_v2.0.0_full_Instance_inverseRelations_OWL_Triples_Identifiers.txt PheKnowLator_v2.0.0_full_Instance_inverseRelations_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.0.0_full_Instance_inverseRelations_OWL_Triples_Integers.txt	Master_Edge_List_Dict.json PheKnowLator_Master_Node_Edge_List_Dict.json PheKnowLator_MergedOntologiesGeneID_Normalized_Cleaned.owl PheKnowLator_v2.0.0_full_Instance_inverseRelations_OWL.owl PheKnowLator_v2.0.0_full_Instance_inverseRelations_noOWL_NodeLabels.txt PheKnowLator_v2.0.0_full_Instance_inverseRelations_noOWL_OWLNETS.nt PheKnowLator_v2.0.0_full_Instance_inverseRelations_noOWL_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.0.0_full_Instance_inverseRelations_noOWL_Triples_Identifiers.txt PheKnowLator_v2.0.0_full_Instance_inverseRelations_noOWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.0.0_full_Instance_inverseRelations_noOWL_Triples_Integers.txt
Class-based Build
Standard Relations		Inverse Relations
OWL	OWL-NETS	OWL	OWL-NETS
Logs
PheKnowLator_v2.0.0_full_subclass_relationsOnly_OWL_Stats.txt PheKnowLator_v2.0.0_full_subclass_relationsOnly_OWL_Stats_Terminal_Output.txt subclass_map_log.json	PheKnowLator_v2.0.0_full_subclass_relationsOnly_noOWL_Stats.txt PheKnowLator_v2.0.0_full_subclass_relationsOnly_noOWL_Stats_Terminal_Output.txt subclass_map_log.json	PheKnowLator_v2.0.0_full_subclass_inverseRelations_OWL_Stats.txt PheKnowLator_v2.0.0_full_subclass_inverseRelations_OWL_Stats_Terminal_Output.txt subclass_map_log.json>	PheKnowLator_v2.0.0_full_subclass_inverseRelations_noOWL_Stats.txt PheKnowLator_v2.0.0_full_subclass_inverseRelations_noOWL_Stats_Terminal_Output.txt 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_Master_Node_Edge_List_Dict.json PheKnowLator_MergedOntologiesGeneID_Normalized_Cleaned.owl PheKnowLator_v2.0.0_full_relationsOnly_OWL.owl PheKnowLator_v2.0.0_full_subclass_relationsOnly_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.0.0_full_subclass_relationsOnly_OWL_NodeLabels.txt PheKnowLator_v2.0.0_full_subclass_relationsOnly_OWL_Triples_Identifiers.txt PheKnowLator_v2.0.0_full_subclass_relationsOnly_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.0.0_full_subclass_relationsOnly_OWL_Triples_Integers.txt	Master_Edge_List_Dict.json PheKnowLator_Master_Node_Edge_List_Dict.json PheKnowLator_MergedOntologiesGeneID_Normalized_Cleaned.owl PheKnowLator_v2.0.0_full_subclass_relationsOnly_OWL.owl PheKnowLator_v2.0.0_full_subclass_relationsOnly_noOWL_NodeLabels.txt PheKnowLator_v2.0.0_full_subclass_relationsOnly_noOWL_OWLNETS.nt PheKnowLator_v2.0.0_full_subclass_relationsOnly_noOWL_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.0.0_full_subclass_relationsOnly_noOWL_Triples_Identifiers.txt PheKnowLator_v2.0.0_full_subclass_relationsOnly_noOWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.0.0_full_subclass_relationsOnly_noOWL_Triples_Integers.txt	Master_Edge_List_Dict.json PheKnowLator_Master_Node_Edge_List_Dict.json PheKnowLator_MergedOntologiesGeneID_Normalized_Cleaned.owl PheKnowLator_v2.0.0_full_inverseRelations_OWL.owl PheKnowLator_v2.0.0_full_subclass_inverseRelations_OWL_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.0.0_full_subclass_inverseRelations_OWL_NodeLabels.txt PheKnowLator_v2.0.0_full_subclass_inverseRelations_OWL_Triples_Identifiers.txt PheKnowLator_v2.0.0_full_subclass_inverseRelations_OWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.0.0_full_subclass_inverseRelations_OWL_Triples_Integers.txt	Master_Edge_List_Dict.json PheKnowLator_Master_Node_Edge_List_Dict.json PheKnowLator_MergedOntologiesGeneID_Normalized_Cleaned.owl PheKnowLator_v2.0.0_full_subclass_inverseRelations_OWL.owl PheKnowLator_v2.0.0_full_subclass_inverseRelations_noOWL_NodeLabels.txt PheKnowLator_v2.0.0_full_subclass_inverseRelations_noOWL_OWLNETS.nt PheKnowLator_v2.0.0_full_subclass_inverseRelations_noOWL_OWLNETS_NetworkxMultiDiGraph.gpickle PheKnowLator_v2.0.0_full_subclass_inverseRelations_noOWL_Triples_Identifiers.txt PheKnowLator_v2.0.0_full_subclass_inverseRelations_noOWL_Triples_Integer_Identifier_Map.json PheKnowLator_v2.0.0_full_subclass_inverseRelations_noOWL_Triples_Integers.txt

---

Return to Top

---