RDF
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.
biocypher:
strict_mode: true
schema_config_path: config/schema_config.yaml
dbms: rdf
### RDF configuration ###
rdf:
rdf_format: turtle
# options: xml, n3, turtle, nt, pretty-xml, trix, trig, nquads, json-ld
rdf_namespaces:
so: http://purl.obolibrary.org/obo/SO_
efo: http://www.ebi.ac.uk/efo/EFO_