In this section, we will learn how to use and implement the output to RDF using the _RDFWriter module.

RDF settings

To write your output to RDF, you have to specify some RDF settings in the biocypher_config.yaml. Using rdf_format, you can choose to export to xml, turtle or any other format rdflib supports. The second configuration is the rdf_namespaces, where you can specify which namespaces exist in your data. If, for instance, your data contain SO (Sequence ontology) terms such as SO:0000001, IDs will be converted into valid URIs to allow referencing. Thus, SO:0000001 will be converted into http://purl.obolibrary.org/obo/SO_0000001. When a node cannot be converted, a default URI will be used (https://biocypher.org/biocypher#<node_id>). Running the pipeline, the _RDFWriter will create a file for every node and relationship type you have specified.

  strict_mode: true
  schema_config_path: config/schema_config.yaml
  dbms: rdf

### RDF configuration ###
  rdf_format: turtle
  # options: xml, n3, turtle, nt, pretty-xml, trix, trig, nquads, json-ld
    so: http://purl.obolibrary.org/obo/SO_
    efo: http://www.ebi.ac.uk/efo/EFO_