Alignment configuration¶

The alignment configuration JSON is a required input that must be placed in the PROJECT_FOLDER/input folder and named as config.json.

Note

The JSON schema and content is validated prior to running the alignment process.

Specification¶

The JSON must contain all of the following properties:

domain_node_type: the type of the domain nodes, e.g. Disease.
seed_ontology_name: the seed ontology name (i.e. the namespace part

of the corresponding node IDs.).
mappings: mapping grouping and directionality specification.
- type_groups: groups the available mapping relations into three
  
  strength categories that are handled differently during the alignment
  
  process; all three type groups must be present.
  equivalence: the strongest mapping relation category; must
  
  contain at least one mapping relation type.
  
  database_reference: the second strongest mapping relation
  
  category that can be an empty list.
  
  label_match: the weakest mapping relation category that can be
  
  an empty list.

Example¶

The alignment configuration JSON.¶

{
  "domain_node_type": "Disease",
  "seed_ontology_name": "MONDO",
  "mappings": {
    "type_groups": {
      "equivalence": ["equivalent_to", "merge"],
      "database_reference": ["database_cross_reference", "xref"],
      "label_match": []
    }
  }
}