scigraph.yaml

graphConfiguration:
    # The location of the graph.
    # If this location does not exist it will be created.
    # Loading will append content to existing graphs.
    location: ../../omnicorp-scigraph
    indexedNodeProperties:
      - category
      - label
      - synonym
      - fragment
    exactNodeProperties:
      - label
      - synonym
#    curies:
#      'rdfs' : 'http://www.w3.org/2000/01/rdf-schema#'
#      'UBERON' : 'http://purl.obolibrary.org/obo/UBERON_'
#      'BSPO' : 'http://purl.obolibrary.org/obo/BSPO_'
#      'PATO' : 'http://purl.obolibrary.org/obo/PATO_'
#      'VTO' : 'http://purl.obolibrary.org/obo/VTO_'
#      'BFO' : 'http://purl.obolibrary.org/obo/BFO_'
#      'TAXRANK' : 'http://purl.obolibrary.org/obo/TAXRANK_'
#      'RO' : 'http://purl.obolibrary.org/obo/RO_'

    # Set Neo4j configuration options
    neo4jConfig:
      dump_configuration : true
      dbms.pagecache.memory : 1G

# The number of threads dedicated to reading ontologies
producerThreadCount: 2

# The number of threads dedicated to processing ontology axioms
consumerThreadCount: 2

# A list of ontologies to import.
ontologies:
  # Files can be local paths...
  - url: ../../ontologies-merged.ttl
    # Or URIs
    #- http://www.w3.org/TR/2004/REC-owl-guide-20040210/wine.rdf
    # And can optionally include a reasoner factory
    #reasonerConfiguration:
    #  factory: org.semanticweb.elk.owlapi.ElkReasonerFactory

# Categories are used for vocabulary term filtering and are inherited to
# subclasses of their parent. They are also added as node labels for
# convenience.
# Note that previously defined curies can be used instead of IRIs.
#categories:
#    UBERON:0001062: anatomical_entity
#    VTO:0000001: taxon
#    PATO:0000001: quality

# All properties are stored but can optionally be added to a new node property.
# Note that previously defined curies can be used instead of IRIs.
mappedProperties:
  - name: label # The name of the new property
    properties: # The list of properties mapped to the new property
    - http://www.w3.org/2000/01/rdf-schema#label
  - name: synonym
    properties:
    - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
    - http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
    - http://www.ebi.ac.uk/efo/alternative_term
#    - http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
#    - http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
#    - http://www.w3.org/2004/02/skos/core#prefLabel
#  - name: comment
#    properties: