merge.yaml

---
configuration:
  output_directory: data/merged
  checkpoint: false
  property_types:
    # define the type for non-canonical node/edge properties
    combined_score: 'xsd:float'
    confidence_score: 'xsd:float'
    neighborhood: 'xsd:float'
    neighborhood_transferred: 'xsd:float'
    fusion: 'xsd:float'
    cooccurence: 'xsd:float'
    homology: 'xsd:float'
    coexpression: 'xsd:float'
    coexpression_transferred: 'xsd:float'
    experiments: 'xsd:float'
    experiments_transferred: 'xsd:float'
    database: 'xsd:float'
    database_transferred: 'xsd:float'
    textmining: 'xsd:float'
    textmining_transferred: 'xsd:float'

merged_graph:
  name: IDG graph
  source:
    atc:
      name: "Anatomical Therapeutic Chemical Classifications"
      input:
        format: tsv
        filename:
          - data/transformed/atc/atc-classes_nodes.tsv
          - data/transformed/atc/atc-classes_edges.tsv
    drug-central-dti:
      name: "DrugCentral Drug-Target Interactions"
      input:
        format: tsv
        filename:
          - data/transformed/drug_central/drugcentral-dti_nodes.tsv
          - data/transformed/drug_central/drugcentral-dti_edges.tsv
    drug-central-atc:
      name: "DrugCentral ATC Codes and Drug Dosages"
      input:
        format: tsv
        filename:
          - data/transformed/drug_central/drugcentral-atc_ddd_nodes.tsv
          - data/transformed/drug_central/drugcentral-atc_ddd_edges.tsv
    drug-central-reference:
      name: "DrugCentral Drug References"
      input:
        format: tsv
        filename:
          - data/transformed/drug_central/drugcentral-reference_nodes.tsv
          - data/transformed/drug_central/drugcentral-reference_edges.tsv
    drug-central-property:
      name: "DrugCentral Drug Properties and References (inc. mentions)"
      input:
        format: tsv
        filename:
          - data/transformed/drug_central/drugcentral-property_nodes.tsv
          - data/transformed/drug_central/drugcentral-property_edges.tsv
    drug-central-approval:
      name: "DrugCentral Drug Regulatory Approval Status"
      input:
        format: tsv
        filename:
          - data/transformed/drug_central/drugcentral-approval_nodes.tsv
          - data/transformed/drug_central/drugcentral-approval_edges.tsv
    drug-central-identifier:
      name: "DrugCentral Drug Identifiers"
      input:
        format: tsv
        filename:
          - data/transformed/drug_central/drugcentral-identifier_nodes.tsv
          - data/transformed/drug_central/drugcentral-identifier_edges.tsv
    drug-central-indications:
      name: "DrugCentral Indications and Other Relationships"
      input:
        format: tsv
        filename:
          - data/transformed/drug_central/drugcentral-omop_relationship_nodes.tsv
          - data/transformed/drug_central/drugcentral-omop_relationship_edges.tsv
    gocams:
      name: "Gene Ontology Causal Activity Modeling"
      input:
        format: tsv
        filename:
          - data/transformed/gocams/gocams-fix-nodes_nodes.tsv
          - data/transformed/gocams/gocams-fix-edges_edges.tsv
    hpa:
      name: "Human Proteome Atlas"
      input:
        format: tsv
        filename:
          - data/transformed/hpa/hpa-data_nodes.tsv
          - data/transformed/hpa/hpa-data_edges.tsv
    omim:
      name: "OMIM Gene to Disease relationships"
      input:
        format: tsv
        filename:
          - data/transformed/omim/omim_nodes.tsv
          - data/transformed/omim/omim_edges.tsv
    chebi:
      name: "Chemical Entities of Biological Interest"
      input:
        format: tsv
        filename:
          - data/transformed/ontologies/chebi_kgx_tsv_nodes.tsv
          - data/transformed/ontologies/chebi_kgx_tsv_edges.tsv
    go:
      name: "Gene Ontology"
      input:
        format: tsv
        filename:
          - data/transformed/ontologies/go_kgx_tsv_nodes.tsv
          - data/transformed/ontologies/go_kgx_tsv_edges.tsv
    hp:
      name: "Human Phenotype Ontology"
      input:
        format: tsv
        filename:
          - data/transformed/ontologies/hp_kgx_tsv_nodes.tsv
          - data/transformed/ontologies/hp_kgx_tsv_edges.tsv
    mondo:
      name: "Mondo Disease Ontology"
      input:
        format: tsv
        filename:
          - data/transformed/ontologies/mondo_kgx_tsv_nodes.tsv
          - data/transformed/ontologies/mondo_kgx_tsv_edges.tsv
    ogms:
      name: "Ontology for General Medical Science"
      input:
        format: tsv
        filename:
          - data/transformed/ontologies/ogms_kgx_tsv_nodes.tsv
          - data/transformed/ontologies/ogms_kgx_tsv_edges.tsv
    orphanet-gene:
      name: "OrphaNet gene to disease"
      input:
        format: tsv
        filename:
          - data/transformed/orphanet/orphanet_gene_nodes.tsv
          - data/transformed/orphanet/orphanet_gene_edges.tsv
    orphanet-phenotype:
      name: "OrphaNet phenotype to disease"
      input:
        format: tsv
        filename:
          - data/transformed/orphanet/orphanet_pheno_nodes.tsv
          - data/transformed/orphanet/orphanet_pheno_edges.tsv
    reactomepathways:
      name: "Reactome - all pathways"
      input:
        format: tsv
        filename:
          - data/transformed/reactome/reactomepathways_nodes.tsv
          - data/transformed/reactome/reactomepathways_edges.tsv
    reactomepathwaysrelation:
      name: "Reactome - relationships between pathways"
      input:
        format: tsv
        filename:
          - data/transformed/reactome/reactomepathwaysrelation_nodes.tsv
          - data/transformed/reactome/reactomepathwaysrelation_edges.tsv
    chebi2reactome:
      name: "Reactome - CHEBI maps"
      input:
        format: tsv
        filename:
          - data/transformed/reactome/chebi2reactome_nodes.tsv
          - data/transformed/reactome/chebi2reactome_edges.tsv
    uniprot2reactome:
      name: "Reactome - UniProtKB maps"
      input:
        format: tsv
        filename:
          - data/transformed/reactome/uniprot2reactome_nodes.tsv
          - data/transformed/reactome/uniprot2reactome_edges.tsv
    tcrd-ids:
      name: "Target Central Resource Database - IDs"
      input:
        format: tsv
        filename:
          - data/transformed/tcrd/tcrd-ids_nodes.tsv
          - data/transformed/tcrd/tcrd-ids_edges.tsv
    # tcrd-protein:
    #   name: "Target Central Resource Database - Proteins"
    #   input:
    #     format: tsv
    #     filename:
    #       - data/transformed/tcrd/tcrd-protein_nodes.tsv
    #       - data/transformed/tcrd/tcrd-protein_edges.tsv
    string:
      name: "STRING"
      input:
        format: tsv
        filename:
          - data/transformed/string/string_nodes.tsv_nodes.tsv
          - data/transformed/string/string_edges.tsv_edges.tsv
    # upheno2:
    #   name: "uPheno2"
    #   input:
    #     format: tsv
    #     filename:
    #       - data/transformed/upheno2/upheno2_edges.tsv
    #       - data/transformed/upheno2/upheno2_nodes.tsv
  operations:
    - name: kgx.graph_operations.summarize_graph.generate_graph_stats
      args:
        graph_name: IDG Graph
        filename: merged_graph_stats.yaml
        node_facet_properties:
          - provided_by
        edge_facet_properties:
          - provided_by
          - source
  destination:
    merged-kg-tsv:
      format: tsv
      filename: merged-kg
#    merged-kg-nt:
#      format: nt
#      compression: gz
#      filename: KG-IDG.nt.gz