From 74a951d90972d4afc7e3b71e5c1a14a2031874c7 Mon Sep 17 00:00:00 2001
From: loesvdbiggelaar <loes@thehyve.nl>
Date: Thu, 18 Apr 2024 16:21:07 +0200
Subject: [PATCH] add some doc

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 create mode 100644 docs/output/RDF.md

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+# Output to 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 e.g. your data contains SO (Sequence ontology) terms, like `SO:0000001`, it will convert the id to a working URI to allow referencing. So `SO:0000001` will be converted into `http://purl.obolibrary.org/obo/SO_0000001`.
+
+```{code-block} yaml
+:caption: biocypher_config.yaml
+
+biocypher:
+  strict_mode: true
+  schema_config_path: config/schema_config.yaml
+  dbms: rdf
+
+### RDF configuration ###
+rdf:
+  rdf_format: turtle # choose: 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_
+
+```
+
+## Output
+The `_RDFWriter` will create a file for every node and relationship type you have specified.