Update README.md

metanetx_uniprot/README.md

@@ -3,7 +3,7 @@
 Code is reused from Biochem4j: https://github.com/neilswainston/biochem4j/tree/master/sbcdb
 
 Access chemical, reaction, enzyme, and organism information from the following sources:
-- libchebipy
+- libchebipy (note, the _parsers.py file found in this repo must be updated for the libchebipy library at ~/libchebipy/_parsers.py)
 - NCBITaxonomy
 - MetaNetX
 - Rhea
@@ -20,3 +20,12 @@ To run and only get reference proteome taxa that also exist in kg-microbe:
 python build_taxa_ids.py ~/biochem4j 1
 ```
 *Note, uses ncbitaxon.json (built from kg-microbe) which is expected to be in the Files directory.
+
+To build the entire graph by combining all separate triples files, and creating a kgx format nodes file:
+```
+python combine_rels.py --directory ~/biochem4j/rels
+python create_labels_file.py --directory ~/biochem4j/rels
+```
+This will output the following files:
+- ~/biochem4j/rels/combined_kg.csv
+- ~/biochem4j/combined_kgx_merged-kg_nodes.csv