merge.yaml

# Sourced from: https://github.com/biolink/kgx/tree/master/examples
---
configuration:
  output_directory: data/merged
  checkpoint: false

merged_graph:
  name: Eco-KG Graph
  source:
    planteome:
      input:
        name: "planteome"
        format: tsv
        filename:
        - data/transformed/Planteome/nodes.tsv
        - data/transformed/Planteome/edges.tsv
    eoltraitbank:
      input:
        name: "EOLTraitBank"
        format: tsv
        filename:
        - data/transformed/EOLTraitBank/nodes.tsv
        - data/transformed/EOLTraitBank/edges.tsv
    geneexpressionatlas:
      input:
        name: "Gene Expression Atlas"
        format: tsv
        filename:
        - data/transformed/Gene Expression Atlas/nodes.tsv
        - data/transformed/Gene Expression Atlas/edges.tsv
    ncbi-ontology:
      input:
        name: "NCBISlim Ontology"
        format: tsv
        filename:
        - data/transformed/ontologies/taxslim_nodes.tsv
        - data/transformed/ontologies/taxslim_edges.tsv
    go-ontology:
      input:
        name: "Gene Ontology"
        format: tsv
        filename:
        - data/transformed/ontologies/go-basic_nodes.tsv
        - data/transformed/ontologies/go-basic_edges.tsv
    to-ontology:
      input:
        name: "Plant Trait Ontology"
        format: tsv
        filename:
        - data/transformed/ontologies/to_nodes.tsv
        - data/transformed/ontologies/to_edges.tsv
    po-ontology:
      input:
        name: "Plant Ontology"
        format: tsv
        filename:
        - data/transformed/ontologies/po_nodes.tsv
        - data/transformed/ontologies/po_edges.tsv
  operations:
    - name: kgx.graph_operations.summarize_graph.generate_graph_stats
      args:
        graph_name: Merged Graph
        filename: merged-kg_stats.yaml
        node_facet_properties:
        edge_facet_properties:
  destination:
    merged-kg-tsv:
      format: tsv
      compression: tar.gz
      filename:
        - merged-kg
#    merged-kg-nt:
#      format: nt
#      compression: gz
#      filename:
#        - merged-kg.nt.gz
#    merged-kg-neo4j:
#      format: neo4j
#      uri: http://localhost:7474
#      username: neo4j
#      password: admin